Representation of a parent sequence that is identified only indirectly (e.g. a protein). More...

#include <OpenMS/METADATA/ID/ParentSequence.h>

Inheritance diagram for ParentSequence:

Collaboration diagram for ParentSequence:

Public Member Functions
	ParentSequence (const String &accession, MoleculeType molecule_type=MoleculeType::PROTEIN, const String &sequence="", const String &description="", double coverage=0.0, bool is_decoy=false, const AppliedProcessingSteps &steps_and_scores=AppliedProcessingSteps())

	ParentSequence (const ParentSequence &)=default

ParentSequence &	merge (const ParentSequence &other)

Public Member Functions inherited from ScoredProcessingResult
AppliedProcessingSteps::nth_index< 1 >::type &	getStepsAndScoresByStep ()
	Return the applied processing steps (incl. scores) as a set ordered by processing step reference (option) More...

const AppliedProcessingSteps::nth_index< 1 >::type &	getStepsAndScoresByStep () const
	Return the applied processing steps (incl. scores) as a set ordered by processing step reference (option) - const variant. More...

void	addProcessingStep (const AppliedProcessingStep &step)
	Add an applied processing step. More...

void	addProcessingStep (ProcessingStepRef step_ref, const std::map< ScoreTypeRef, double > &scores=std::map< ScoreTypeRef, double >())
	Add a processing step (and associated scores, if any) More...

void	addScore (ScoreTypeRef score_type, double score, const std::optional< ProcessingStepRef > &processing_step_opt=std::nullopt)
	Add a score (possibly connected to a processing step) More...

ScoredProcessingResult &	merge (const ScoredProcessingResult &other)
	Merge in data from another object. More...

std::pair< double, bool >	getScore (ScoreTypeRef score_ref) const
	Look up a score by score type. More...

std::pair< double, bool >	getScore (ScoreTypeRef score_ref, std::optional< ProcessingStepRef > processing_step_opt) const
	Look up a score by score type and processing step. More...

std::tuple< double, std::optional< ProcessingStepRef >, bool >	getScoreAndStep (ScoreTypeRef score_ref) const
	Look up a score and associated processing step by score type. More...

std::tuple< double, std::optional< ScoreTypeRef >, bool >	getMostRecentScore () const
	Get the (primary) score from the most recent processing step. More...

Size	getNumberOfScores () const
	Return the number of scores associated with this result. 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...

void	swap (MetaInfoInterface &rhs)
	Swap contents. 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...

DataValue	getMetaValue (const 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 More...

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

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 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...

Public Attributes
String	accession

enum MoleculeType	molecule_type

String	sequence

String	description

double	coverage
	sequence coverage as a fraction between 0 and 1 More...

bool	is_decoy

Public Attributes inherited from ScoredProcessingResult
AppliedProcessingSteps	steps_and_scores

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 ScoredProcessingResult
	ScoredProcessingResult (const AppliedProcessingSteps &steps_and_scores=AppliedProcessingSteps())
	Constructor. More...

	ScoredProcessingResult (const ScoredProcessingResult &)=default
	Copy c'tor. 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 parent sequence that is identified only indirectly (e.g. a protein).

Constructor & Destructor Documentation

◆ ParentSequence() [1/2]

ParentSequence	(	const String &	accession,
		MoleculeType	molecule_type = `MoleculeType::PROTEIN`,
		const String &	sequence = `""`,
		const String &	description = `""`,
		double	coverage = `0.0`,
		bool	is_decoy = `false`,
		const AppliedProcessingSteps &	steps_and_scores = `AppliedProcessingSteps()`
	)

inlineexplicit

◆ ParentSequence() [2/2]

ParentSequence ( const ParentSequence & )

default

Member Function Documentation

◆ merge()

ParentSequence& merge ( const ParentSequence & other )

inline

References ParentSequence::description, ParentSequence::is_decoy, ScoredProcessingResult::merge(), and ParentSequence::sequence.

Member Data Documentation

◆ accession

String accession

Referenced by IdentificationDataConverter::exportParentSequenceToMzTab_().

◆ coverage

double coverage

sequence coverage as a fraction between 0 and 1

Referenced by IdentificationDataConverter::exportParentSequenceToMzTab_().

◆ description

String description

Referenced by IdentificationDataConverter::exportParentSequenceToMzTab_(), and ParentSequence::merge().

◆ is_decoy

bool is_decoy

Referenced by ParentSequence::merge().

◆ molecule_type

enum MoleculeType molecule_type

◆ sequence

String sequence