Representation of a protein hit. More...

#include <OpenMS/METADATA/ProteinHit.h>

Inheritance diagram for ProteinHit:

Collaboration diagram for ProteinHit:

Classes
class	ProteinHitAccessionHash
	Hash of a ProteinHit based on its accession only! More...

class	ProteinHitPtrAccessionHash

class	ScoreLess
	Lesser predicate for scores of hits. More...

class	ScoreMore
	Greater predicate for scores of hits. More...

Public Member Functions
Constructors and Destructor
	ProteinHit ()
	Default constructor. More...

	ProteinHit (double score, UInt rank, String accession, String sequence)
	Values constructor. More...

	ProteinHit (const ProteinHit &)=default
	Copy constructor. More...

	ProteinHit (ProteinHit &&)=default
	Move constructor. More...

ProteinHit &	operator= (const ProteinHit &)=default
	Assignment operator. More...

ProteinHit &	operator= (ProteinHit &&)=default
	Move 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...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move 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 DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...

const DataValue &	getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to an index, or a default value (default: 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	addMetaValues (const MetaInfoInterface &from)
	function to copy all meta values from one object to this one 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

Accessors
double	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...

std::set< std::pair< Size, ResidueModification > >	modifications_
	modified positions in a protein More...

double	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...

const std::set< std::pair< Size, ResidueModification > > &	getModifications () const
	returns the set of modified protein positions More...

void	setModifications (std::set< std::pair< Size, ResidueModification > > &mods)
	sets the set of modified protein positions 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...

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Detailed Description

Representation of a protein hit.

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

Constructor & Destructor Documentation

◆ ProteinHit() [1/4]

ProteinHit ( )

Default constructor.

◆ ProteinHit() [2/4]

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

Values constructor.

◆ ProteinHit() [3/4]

ProteinHit ( const ProteinHit & )

default

Copy constructor.

◆ ProteinHit() [4/4]

ProteinHit ( ProteinHit && )

default

Move constructor.

Member Function Documentation

◆ getAccession()

const String& getAccession ( ) const

returns the accession of the protein

Referenced by ConsensusMapMergerAlgorithm::accessionEqual_(), IDMergerAlgorithm::accessionEqual_(), ConsensusMapMergerAlgorithm::accessionHash_(), IDMergerAlgorithm::accessionHash_(), ProteinHit::ProteinHitAccessionHash::operator()(), ProteinHit::ProteinHitPtrAccessionHash::operator()(), PercolatorFeatureSetHelper::lq_ProteinHit::operator()(), IDBoostGraph::LabelVisitor::operator()(), IDBoostGraph::PrintAddressVisitor< CharT >::operator()(), IDFilter::HasMatchingAccessionUnordered< HitType >::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

◆ getModifications()

const std::set<std::pair<Size, ResidueModification> >& getModifications ( ) const

returns the set of modified protein positions

◆ getRank()

UInt getRank ( ) const

returns the rank of the protein hit

◆ getScore()

double getScore ( ) const

returns the score of the protein hit

Referenced by IDScoreGetterSetter::getScores_(), and IDBoostGraph::GetPosteriorVisitor::operator()().

◆ getSequence()

const String& getSequence ( ) const

returns the protein sequence

◆ operator!=()

bool operator!= ( const ProteinHit & rhs ) const

Inequality operator.

◆ operator=() [1/3]

ProteinHit& operator= ( const MetaInfoInterface & source )

Assignment for MetaInfo.

◆ operator=() [2/3]

ProteinHit& operator= ( const ProteinHit & )

default

Assignment operator.

◆ operator=() [3/3]

ProteinHit& operator= ( ProteinHit && )

default

Move assignment operator.

◆ 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().

◆ setModifications()

void setModifications ( std::set< std::pair< Size, ResidueModification > > & mods )

sets the set of modified protein positions

◆ setRank()

void setRank ( UInt newrank )

sets the rank

◆ setScore()

void setScore ( const double score )

sets the score of the protein hit

Referenced by IDBoostGraph::SetPosteriorVisitor::operator()().

◆ 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

◆ modifications_

std::set<std::pair<Size, ResidueModification> > modifications_

protected

modified positions in a protein

◆ rank_

UInt rank_

protected

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

◆ score_

double score_

protected

the score of the protein hit

◆ sequence_

String sequence_

protected

the amino acid sequence of the protein hit

Classes

Public Member Functions

Static Public Attributes

Accessors

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProteinHit() [1/4]

◆ ProteinHit() [2/4]

◆ ProteinHit() [3/4]

◆ ProteinHit() [4/4]

Member Function Documentation

◆ getAccession()

◆ getCoverage()

◆ getDescription()

◆ getModifications()

◆ getRank()

◆ getScore()

◆ getSequence()

◆ operator!=()

◆ operator=() [1/3]

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ operator==()

◆ setAccession()

◆ setCoverage()

◆ setDescription()

◆ setModifications()

◆ setRank()

◆ setScore()

◆ setSequence()

Member Data Documentation

◆ accession_

◆ coverage_

◆ COVERAGE_UNKNOWN

◆ modifications_

◆ rank_

◆ score_

◆ sequence_