A basic LC-MS feature. More...

#include <OpenMS/KERNEL/BaseFeature.h>

Inheritance diagram for BaseFeature:

Classes
struct	QualityLess
	Compare by quality. More...

Public Member Functions
WidthType	getWidth () const
	Non-mutable access to the features width (full width at half max, FWHM)

void	setWidth (WidthType fwhm)
	Set the width of the feature (FWHM)

const ChargeType &	getCharge () const
	Non-mutable access to charge state.

void	setCharge (const ChargeType &ch)
	Set charge state.

BaseFeature &	operator= (const BaseFeature &rhs)=default
	Assignment operator.

BaseFeature &	operator= (BaseFeature &&rhs) &=default
	Move Assignment operator.

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

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

AnnotationState	getAnnotationState () const
	state of peptide identifications attached to this feature. If one ID has multiple hits, the output depends on the top-hit only

Constructors and Destructor
Default constructor
	BaseFeature ()

	BaseFeature (const BaseFeature &feature)=default
	Copy constructor.

	BaseFeature (BaseFeature &&feature) noexcept

	BaseFeature (const BaseFeature &rhs, UInt64 map_index)
	Copy constructor with a new map_index.

	BaseFeature (const Peak2D &point)
	Constructor from raw data point.

	BaseFeature (const RichPeak2D &point)
	Constructor from raw data point with meta information.

	BaseFeature (const FeatureHandle &fh)
	Constructor from a featurehandle.

	~BaseFeature () override
	Destructor.

Quality methods
Non-mutable access to the overall quality
QualityType	getQuality () const

void	setQuality (QualityType q)
	Set the overall quality.

Functions for dealing with identifications in legacy format
returns a const reference to the PeptideIdentification vector
const PeptideIdentificationList &	getPeptideIdentifications () const

PeptideIdentificationList &	getPeptideIdentifications ()
	returns a mutable reference to the PeptideIdentification vector

void	setPeptideIdentifications (const PeptideIdentificationList &peptides)
	sets the PeptideIdentification vector

void	sortPeptideIdentifications ()
	Sorts the peptide identifications of this feature by the score of their best hit.

Functions for dealing with identifications in new format
has a primary ID (peptide, RNA, compound) been assigned?
bool	hasPrimaryID () const

const IdentificationData::IdentifiedMolecule &	getPrimaryID () const
	Return the primary ID (peptide, RNA, compound) assigned to this feature.

void	clearPrimaryID ()
	clear any primary ID that was assigned

void	setPrimaryID (const IdentificationData::IdentifiedMolecule &id)
	set the primary ID (peptide, RNA, compound) for this feature

const std::set< IdentificationData::ObservationMatchRef > &	getIDMatches () const
	immutable access to the set of matches (e.g. PSMs) with IDs for this feature

std::set< IdentificationData::ObservationMatchRef > &	getIDMatches ()
	mutable access to the set of matches (e.g. PSMs) with IDs for this feature

void	addIDMatch (IdentificationData::ObservationMatchRef ref)
	add an ID match (e.g. PSM) for this feature

void	updateIDReferences (const IdentificationData::RefTranslator &trans)
	Update ID references (primary ID, matches) for this feature.

Public Member Functions inherited from RichPeak2D
	RichPeak2D ()
	Default constructor.

	RichPeak2D (const RichPeak2D &p)=default
	Copy constructor.

	RichPeak2D (const Peak2D &p)
	Constructor from Peak2D.

	RichPeak2D (const PositionType &pos, const IntensityType in)
	Member constructor.

	RichPeak2D (RichPeak2D &&p)=default
	Move constructor.

	~RichPeak2D () override
	Destructor.

RichPeak2D &	operator= (const RichPeak2D &rhs)=default
	Assignment operator.

RichPeak2D &	operator= (RichPeak2D &&rhs) &=default
	Move Assignment operator.

RichPeak2D &	operator= (const Peak2D &rhs)
	Assignment operator.

bool	operator== (const RichPeak2D &rhs) const
	Equality operator.

bool	operator!= (const RichPeak2D &rhs) const
	Equality operator.

Public Member Functions inherited from Peak2D
bool	operator== (const Peak2D &rhs) const =default
	Equality operator.

bool	operator!= (const Peak2D &rhs) const
	Equality operator.

	Peak2D ()=default

	Peak2D (const PositionType &pos, const IntensityType in)
	Member constructor.

	Peak2D (const Peak2D &p)=default
	Copy constructor.

	Peak2D (Peak2D &&) noexcept=default
	Move constructor.

Peak2D &	operator= (const Peak2D &rhs)=default
	Assignment operator.

Peak2D &	operator= (Peak2D &&) noexcept=default
	Move assignment operator.

	~Peak2D () noexcept=default
	Destructor.

IntensityType	getIntensity () const

void	setIntensity (IntensityType intensity)
	Sets data point intensity (height)

PositionType const &	getPosition () const
	Non-mutable access to the position.

PositionType &	getPosition ()
	Mutable access to the position.

void	setPosition (const PositionType &position)
	Mutable access to the position.

CoordinateType	getMZ () const
	Returns the m/z coordinate (index 1)

void	setMZ (CoordinateType coordinate)
	Mutable access to the m/z coordinate (index 1)

CoordinateType	getRT () const
	Returns the RT coordinate (index 0)

void	setRT (CoordinateType coordinate)
	Mutable access to the RT coordinate (index 0)

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.

Public Member Functions inherited from UniqueIdInterface
	UniqueIdInterface ()
	Default constructor - the unique id will be invalid

	UniqueIdInterface (const UniqueIdInterface &rhs)=default
	Copy constructor - copies the unique id.

	UniqueIdInterface (UniqueIdInterface &&rhs)=default
	Move constructor.

UniqueIdInterface &	operator= (UniqueIdInterface const &rhs)=default
	Assignment operator - copies the unique id.

UniqueIdInterface &	operator= (UniqueIdInterface &&) &=default
	Move Assignment operator - copies the unique id.

virtual	~UniqueIdInterface ()=default
	Destructor.

bool	operator== (UniqueIdInterface const &rhs) const
	Equality comparison operator - the unique ids must be equal (!)

UInt64	getUniqueId () const
	Non-mutable access to unique id - returns the unique id.

Size	clearUniqueId ()
	Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise.

void	swap (UniqueIdInterface &from)

Size	hasValidUniqueId () const
	Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise.

Size	hasInvalidUniqueId () const
	Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise.

Size	setUniqueId ()
	Assigns a new, valid unique id. Always returns 1.

Size	ensureUniqueId ()
	Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise.

void	setUniqueId (UInt64 rhs)
	Assigns the given unique id.

void	setUniqueId (const std::string &rhs)
	Mutable access to unique id.

Protected Attributes
QualityType	quality_
	Overall quality measure of the feature.

ChargeType	charge_
	Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state.

WidthType	width_
	Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model.

PeptideIdentificationList	peptides_
	PeptideIdentifications belonging to the feature.

std::optional< IdentificationData::IdentifiedMolecule >	primary_id_
	primary ID (peptide, RNA, compound) assigned to this feature

std::set< IdentificationData::ObservationMatchRef >	id_matches_
	set of observation matches (e.g. PSMs) with IDs for this feature

Protected Attributes inherited from Peak2D
PositionType	position_ {}
	The data point position.

IntensityType	intensity_ {}
	The data point intensity.

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

Protected Attributes inherited from UniqueIdInterface
UInt64	unique_id_
	the unique id

Type definitions
Type of quality values
enum class	AnnotationState { FEATURE_ID_NONE , FEATURE_ID_SINGLE , FEATURE_ID_MULTIPLE_SAME , FEATURE_ID_MULTIPLE_DIVERGENT , SIZE_OF_ANNOTATIONSTATE }
	state of identification, use getAnnotationState() to query it More...

typedef float	QualityType

typedef Int	ChargeType
	Type of charge values.

typedef float	WidthType
	Type of feature width/FWHM (RT)

static const std::string	NamesOfAnnotationState [static_cast< size_t >(AnnotationState::SIZE_OF_ANNOTATIONSTATE)]

Additional Inherited Members
Public Types inherited from Peak2D
using	IntensityType = float
	Intensity type.

using	CoordinateType = double
	Coordinate type (of the position)

using	PositionType = DPosition< 2 >
	Position type.

enum	DimensionDescription { RT = 0 , MZ = 1 , DIMENSION = 2 }
	This enum maps the symbolic names of the dimensions to numbers. More...

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

Public Types inherited from UniqueIdInterface
enum	{ INVALID = 0 }
	This is the invalid unique id (cast it to a UInt64 if you like) More...

Static Public Member Functions inherited from Peak2D
static char const *	shortDimensionName (UInt const dim)
	Short name of the dimension (abbreviated form)

static char const *	shortDimensionNameRT ()
	Short name of the dimension (abbreviated form)

static char const *	shortDimensionNameMZ ()
	Short name of the dimension (abbreviated form)

static char const *	fullDimensionName (UInt const dim)
	Full name of the dimension (self-explanatory form)

static char const *	fullDimensionNameRT ()
	Full name of the dimension (self-explanatory form)

static char const *	fullDimensionNameMZ ()
	Full name of the dimension (self-explanatory form)

static char const *	shortDimensionUnit (UInt const dim)
	Unit of measurement (abbreviated form)

static char const *	shortDimensionUnitRT ()
	Unit of measurement (abbreviated form)

static char const *	shortDimensionUnitMZ ()
	Unit of measurement (abbreviated form)

static char const *	fullDimensionUnit (UInt const dim)
	Unit of measurement (self-explanatory form)

static char const *	fullDimensionUnitRT ()
	Unit of measurement (self-explanatory form)

static char const *	fullDimensionUnitMZ ()
	Unit of measurement (self-explanatory form)

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

Static Public Member Functions inherited from UniqueIdInterface
static bool	isValid (UInt64 unique_id)
	Returns true if the unique_id is valid, false otherwise.

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

Static Protected Attributes inherited from Peak2D
static char const *const	dimension_name_short_ [DIMENSION]
	Short name of the dimension (abbreviated form)

static char const *const	dimension_name_full_ [DIMENSION]
	Full name of the dimension (self-explanatory form)

static char const *const	dimension_unit_short_ [DIMENSION]
	Unit of measurement (abbreviated form)

static char const *const	dimension_unit_full_ [DIMENSION]
	Unit of measurement (self-explanatory form)

Detailed Description

A basic LC-MS feature.

This class represents a "minimal" feature, defined by a position in RT and m/z, intensity, charge, quality, and annotated peptides. Most classes dealing with features will use the subclasses Feature or ConsensusFeature directly. However, algorithms that rely on very general characteristics of features can use this class to provide a unified solution for both "normal" features and consensus features.

Member Typedef Documentation

◆ ChargeType

typedef Int ChargeType

Type of charge values.

◆ QualityType

typedef float QualityType

◆ WidthType

typedef float WidthType

Type of feature width/FWHM (RT)

Member Enumeration Documentation

◆ AnnotationState

enum class AnnotationState

strong

state of identification, use getAnnotationState() to query it

Enumerator
FEATURE_ID_NONE
FEATURE_ID_SINGLE
FEATURE_ID_MULTIPLE_SAME
FEATURE_ID_MULTIPLE_DIVERGENT
SIZE_OF_ANNOTATIONSTATE

Constructor & Destructor Documentation

◆ BaseFeature() [1/7]

BaseFeature ( )

◆ BaseFeature() [2/7]

BaseFeature ( const BaseFeature & feature )

default

Copy constructor.

◆ BaseFeature() [3/7]

BaseFeature ( BaseFeature && feature )

inlinenoexcept

Move constructor Note: can't be "noexcept = default" because of missing noexcept on some standard containers so we need to explicitly define it noexcept and provide an implementation.

◆ BaseFeature() [4/7]

BaseFeature	(	const BaseFeature &	rhs,
		UInt64	map_index
	)

Copy constructor with a new map_index.

◆ BaseFeature() [5/7]

BaseFeature ( const Peak2D & point )

explicit

Constructor from raw data point.

◆ BaseFeature() [6/7]

BaseFeature ( const RichPeak2D & point )

explicit

Constructor from raw data point with meta information.

◆ BaseFeature() [7/7]

BaseFeature ( const FeatureHandle & fh )

explicit

Constructor from a featurehandle.

◆ ~BaseFeature()

~BaseFeature ( )

override

Destructor.

Member Function Documentation

◆ addIDMatch()

void addIDMatch ( IdentificationData::ObservationMatchRef ref )

add an ID match (e.g. PSM) for this feature

◆ clearPrimaryID()

void clearPrimaryID ( )

clear any primary ID that was assigned

◆ getAnnotationState()

AnnotationState getAnnotationState ( ) const

state of peptide identifications attached to this feature. If one ID has multiple hits, the output depends on the top-hit only

◆ getCharge()

const ChargeType & getCharge ( ) const

Non-mutable access to charge state.

Referenced by MQEvidence::exportRowFromFeature_(), and MQMsms::exportRowFromFeature_().

◆ getIDMatches() [1/2]

std::set< IdentificationData::ObservationMatchRef > & getIDMatches ( )

mutable access to the set of matches (e.g. PSMs) with IDs for this feature

◆ getIDMatches() [2/2]

const std::set< IdentificationData::ObservationMatchRef > & getIDMatches ( ) const

immutable access to the set of matches (e.g. PSMs) with IDs for this feature

◆ getPeptideIdentifications() [1/2]

PeptideIdentificationList & getPeptideIdentifications ( )

returns a mutable reference to the PeptideIdentification vector

◆ getPeptideIdentifications() [2/2]

const PeptideIdentificationList & getPeptideIdentifications ( ) const

Referenced by MQEvidence::exportRowFromFeature_(), MQMsms::exportRowFromFeature_(), MQExporterHelper::hasPeptideIdentifications_(), MQExporterHelper::hasValidPepID_(), MQExporterHelper::MQCommonOutputs::MQCommonOutputs(), and FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides::operator()().

◆ getPrimaryID()

const IdentificationData::IdentifiedMolecule & getPrimaryID ( ) const

Return the primary ID (peptide, RNA, compound) assigned to this feature.

Exceptions

Exception::MissingInformation if no ID was assigned

◆ getQuality()

QualityType getQuality ( ) const

Referenced by BaseFeature::QualityLess::operator()(), BaseFeature::QualityLess::operator()(), and BaseFeature::QualityLess::operator()().

◆ getWidth()

WidthType getWidth ( ) const

Non-mutable access to the features width (full width at half max, FWHM)

Referenced by MQEvidence::exportRowFromFeature_().

◆ hasPrimaryID()

bool hasPrimaryID ( ) const

◆ operator!=()

bool operator!= ( const BaseFeature & rhs ) const

Inequality operator.

◆ operator=() [1/2]

BaseFeature & operator= ( BaseFeature && rhs ) &

default

Move Assignment operator.

◆ operator=() [2/2]

BaseFeature & operator= ( const BaseFeature & rhs )

default

Assignment operator.

◆ operator==()

bool operator== ( const BaseFeature & rhs ) const

Equality operator.

◆ setCharge()

void setCharge ( const ChargeType & ch )

Set charge state.

Referenced by MsInspectFile::load(), and SpecArrayFile::load().

◆ setPeptideIdentifications()

void setPeptideIdentifications ( const PeptideIdentificationList & peptides )

sets the PeptideIdentification vector

◆ setPrimaryID()

void setPrimaryID ( const IdentificationData::IdentifiedMolecule & id )

set the primary ID (peptide, RNA, compound) for this feature

◆ setQuality()

void setQuality ( QualityType q )

Set the overall quality.

◆ setWidth()

void setWidth ( WidthType fwhm )

Set the width of the feature (FWHM)

◆ sortPeptideIdentifications()

void sortPeptideIdentifications ( )

Sorts the peptide identifications of this feature by the score of their best hit.

First the hits of every identification are sorted with PeptideIdentification::sort(), so afterwards the best hit of each identification is its first hit. Then the identifications are ordered best first: the identification whose first hit has the best score ends up at index 0. Identifications without hits are placed after all identifications with hits. Identifications whose first hits score equally, and identifications without hits among themselves, keep their relative order (the sort is stable).

Note: The identifications are assumed to share one score type. The score orientation used to compare them is read once, from the first identification (in the order before sorting) that has hits, or is higher-is-better if no identification has hits. An identification with a different orientation is ordered by that single orientation rather than rejected; only the order of its own hits follows its own orientation. With mixed orientations the result therefore depends on the order before sorting, and sorting again can change it; the sort is idempotent only when all identifications share one orientation.

◆ updateIDReferences()

void updateIDReferences ( const IdentificationData::RefTranslator & trans )

Update ID references (primary ID, matches) for this feature.

This is needed e.g. after the IdentificationData instance containing the referenced data has been copied.

Member Data Documentation

◆ charge_

ChargeType charge_

protected

Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state.

◆ id_matches_

std::set<IdentificationData::ObservationMatchRef> id_matches_

protected

set of observation matches (e.g. PSMs) with IDs for this feature

◆ NamesOfAnnotationState

const std::string NamesOfAnnotationState[static_cast< size_t >(AnnotationState::SIZE_OF_ANNOTATIONSTATE)]

static

◆ peptides_

PeptideIdentificationList peptides_

protected

PeptideIdentifications belonging to the feature.

◆ primary_id_

std::optional<IdentificationData::IdentifiedMolecule> primary_id_

protected

primary ID (peptide, RNA, compound) assigned to this feature

◆ quality_

QualityType quality_

protected

Overall quality measure of the feature.

◆ width_

WidthType width_

protected

Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model.

Classes

Public Member Functions

Protected Attributes

Type definitions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ChargeType

◆ QualityType

◆ WidthType

Member Enumeration Documentation

◆ AnnotationState

Constructor & Destructor Documentation

◆ BaseFeature() [1/7]

◆ BaseFeature() [2/7]

◆ BaseFeature() [3/7]

◆ BaseFeature() [4/7]

◆ BaseFeature() [5/7]

◆ BaseFeature() [6/7]

◆ BaseFeature() [7/7]

◆ ~BaseFeature()

Member Function Documentation

◆ addIDMatch()

◆ clearPrimaryID()

◆ getAnnotationState()

◆ getCharge()

◆ getIDMatches() [1/2]

◆ getIDMatches() [2/2]

◆ getPeptideIdentifications() [1/2]

◆ getPeptideIdentifications() [2/2]

◆ getPrimaryID()

◆ getQuality()

◆ getWidth()

◆ hasPrimaryID()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setCharge()

◆ setPeptideIdentifications()

◆ setPrimaryID()

◆ setQuality()

◆ setWidth()

◆ sortPeptideIdentifications()

◆ updateIDReferences()

Member Data Documentation

◆ charge_

◆ id_matches_

◆ NamesOfAnnotationState

◆ peptides_

◆ primary_id_

◆ quality_

◆ width_