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 Types
enum class	TargetDecoyType { TARGET , DECOY , UNKNOWN }
	Enum for target/decoy annotation. More...

Public Types inherited from MetaInfoInterface
using	MetaInfoConstIterator = MetaInfo::const_iterator
	Const iterator type for iterating over meta info entries.

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

	ProteinHit (double score, UInt rank, std::string accession, std::string sequence)
	Values constructor.

	ProteinHit (const ProteinHit &)=default
	Copy constructor.

	ProteinHit (ProteinHit &&)=default
	Move constructor.

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

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

ProteinHit &	operator= (const MetaInfoInterface &source)
	Assignment for MetaInfo.

bool	operator== (const ProteinHit &rhs) const
	Equality operator.

bool	operator!= (const ProteinHit &rhs) const
	Inequality operator.

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.

	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.

	~MetaInfoInterface ()
	Destructor.

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

MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.

void	swap (MetaInfoInterface &rhs)
	Swap contents.

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.

const DataValue &	getMetaValue (const std::string &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.

DataValue	getMetaValue (const std::string &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.

DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found

bool	metaValueExists (const std::string &name) const
	Returns whether an entry with the given name exists.

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.

void	setMetaValue (const std::string &name, const DataValue &value)
	Sets the DataValue corresponding to a name.

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.

void	removeMetaValue (const std::string &name)
	Removes the DataValue corresponding to `name` if it exists.

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists.

void	addMetaValues (const MetaInfoInterface &from)

void	getKeys (std::vector< std::string > &keys) const
	Fills the given vector with a list of all keys for which a value is set.

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.

void	clearMetaInfo ()
	Removes all meta values.

MetaInfoConstIterator	metaBegin () const
	Returns a const iterator to the beginning of the meta info entries.

MetaInfoConstIterator	metaEnd () const
	Returns a const iterator to the end of the meta info entries.

Size	metaSize () const
	Returns the number of meta info entries.

Static Public Attributes
static const double	COVERAGE_UNKNOWN

Accessors
double	score_
	the score of the protein hit

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

std::string	accession_
	the protein identifier

std::string	sequence_
	the amino acid sequence of the protein hit

double	coverage_
	coverage of the protein based upon the matched peptide sequences

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

double	getScore () const
	returns the score of the protein hit

UInt	getRank () const
	returns the rank of the protein hit

const std::string &	getSequence () const
	returns the protein sequence

const std::string &	getAccession () const
	returns the accession of the protein

std::string	getDescription () const
	returns the description of the protein

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

void	setScore (const double score)
	sets the score of the protein hit

void	setRank (UInt newrank)
	sets the rank

void	setSequence (const std::string &sequence)
	sets the protein sequence

void	setSequence (std::string &&sequence)

void	setAccession (const std::string &accession)
	sets the accession of the protein

void	setDescription (const std::string &description)
	sets the description of the protein

void	setCoverage (const double coverage)
	sets the coverage (in percent) of the protein hit based upon matched peptides

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

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

bool	isDecoy () const
	returns true if this is a decoy hit (false for TARGET and UNKNOWN)

void	setTargetDecoyType (TargetDecoyType type)
	Sets the target/decoy type for this protein hit.

TargetDecoyType	getTargetDecoyType () const
	Returns the target/decoy type for this protein hit.

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry.

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_ = nullptr
	Pointer to the MetaInfo object.

Detailed Description

Representation of a protein hit.

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

Member Enumeration Documentation

◆ TargetDecoyType

enum class TargetDecoyType

strong

Enum for target/decoy annotation.

Enumerator
TARGET	Target protein.
DECOY	Decoy protein.
UNKNOWN	Target/decoy status is unknown (meta value not set)

Constructor & Destructor Documentation

◆ ProteinHit() [1/4]

ProteinHit ( )

Default constructor.

◆ ProteinHit() [2/4]

ProteinHit	(	double	score,
		UInt	rank,
		std::string	accession,
		std::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 std::string & getAccession ( ) const

returns the accession of the protein

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

◆ getCoverage()

double getCoverage ( ) const

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

◆ getDescription()

std::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_(), IDBoostGraph::GetPosteriorVisitor::operator()(), and IDBoostGraph::GetScoreTgTVisitor::operator()().

◆ getSequence()

const std::string & getSequence ( ) const

returns the protein sequence

◆ getTargetDecoyType()

TargetDecoyType getTargetDecoyType ( ) const

Returns the target/decoy type for this protein hit.

This method performs case-insensitive parsing of the "target_decoy" meta value and returns the corresponding enum value. Returns UNKNOWN if the meta value does not exist.

Returns

The target/decoy classification:

TARGET: Target protein
DECOY: Decoy protein
UNKNOWN: Target/decoy status not set (meta value missing)

◆ isDecoy()

bool isDecoy ( ) const

returns true if this is a decoy hit (false for TARGET and UNKNOWN)

◆ 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 std::string & accession )

sets the accession of the protein

◆ setCoverage()

void setCoverage ( const double coverage )

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

◆ setDescription()

void setDescription ( const std::string & description )

sets the description of the protein

◆ 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() [1/2]

void setSequence ( const std::string & sequence )

sets the protein sequence

◆ setSequence() [2/2]

void setSequence ( std::string && sequence )

◆ setTargetDecoyType()

void setTargetDecoyType ( TargetDecoyType type )

Sets the target/decoy type for this protein hit.

This method provides a type-safe way to annotate protein hits with their target/decoy status.

Parameters

[in]

type

The target/decoy classification:

TARGET: Target protein
DECOY: Decoy protein
UNKNOWN: Target/decoy status is unknown; the "target_decoy" meta value is removed

Member Data Documentation

◆ accession_

std::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_

std::string sequence_

protected

the amino acid sequence of the protein hit

Classes

Public Types

Public Member Functions

Static Public Attributes

Accessors

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ TargetDecoyType

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()

◆ getTargetDecoyType()

◆ isDecoy()

◆ operator!=()

◆ operator=() [1/3]

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ operator==()

◆ setAccession()

◆ setCoverage()

◆ setDescription()

◆ setModifications()

◆ setRank()

◆ setScore()

◆ setSequence() [1/2]

◆ setSequence() [2/2]

◆ setTargetDecoyType()

Member Data Documentation

◆ accession_

◆ coverage_

◆ COVERAGE_UNKNOWN

◆ modifications_

◆ rank_

◆ score_

◆ sequence_