Feature Class Reference

An LC-MS feature. More...

#include <OpenMS/KERNEL/Feature.h>

Inheritance diagram for Feature:

Collaboration diagram for Feature:

Public Member Functions
Constructors and Destructor
	Feature ()
	Default constructor. More...
	Feature (const BaseFeature &base)
	explicit C'tor from BaseFeature More...
	Feature (const Feature &feature)
	Copy constructor. More...
	Feature (Feature &&) noexcept
	Move constructor. More...
	~Feature () override
	Destructor. More...
Public Member Functions inherited from BaseFeature
WidthType	getWidth () const
	Non-mutable access to the features width (full width at half max, FWHM) More...
void	setWidth (WidthType fwhm)
	Set the width of the feature (FWHM) More...
const ChargeType &	getCharge () const
	Non-mutable access to charge state. More...
void	setCharge (const ChargeType &ch)
	Set charge state. More...
BaseFeature &	operator= (const BaseFeature &rhs)=default
	Assignment operator. More...
BaseFeature &	operator= (BaseFeature &&rhs) &=default
	Move Assignment operator. More...
bool	operator== (const BaseFeature &rhs) const
	Equality operator. More...
bool	operator!= (const BaseFeature &rhs) const
	Inequality operator. More...
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 More...
	BaseFeature ()
	BaseFeature (const BaseFeature &feature)=default
	Copy constructor. More...
	BaseFeature (BaseFeature &&feature) noexcept
	BaseFeature (const BaseFeature &rhs, UInt64 map_index)
	Copy constructor with a new map_index. More...
	BaseFeature (const Peak2D &point)
	Constructor from raw data point. More...
	BaseFeature (const RichPeak2D &point)
	Constructor from raw data point with meta information. More...
	BaseFeature (const FeatureHandle &fh)
	Constructor from a featurehandle. More...
	~BaseFeature () override
	Destructor. More...
QualityType	getQuality () const
void	setQuality (QualityType q)
	Set the overall quality. More...
const std::vector< PeptideIdentification > &	getPeptideIdentifications () const
std::vector< PeptideIdentification > &	getPeptideIdentifications ()
	returns a mutable reference to the PeptideIdentification vector More...
void	setPeptideIdentifications (const std::vector< PeptideIdentification > &peptides)
	sets the PeptideIdentification vector More...
void	sortPeptideIdentifications ()
	sorts PeptideIdentifications, assuming they have the same scoreType. More...
bool	hasPrimaryID () const
const IdentificationData::IdentifiedMolecule &	getPrimaryID () const
	Return the primary ID (peptide, RNA, compound) assigned to this feature. More...
void	clearPrimaryID ()
	clear any primary ID that was assigned More...
void	setPrimaryID (const IdentificationData::IdentifiedMolecule &id)
	set the primary ID (peptide, RNA, compound) for this feature More...
const std::set< IdentificationData::ObservationMatchRef > &	getIDMatches () const
	immutable access to the set of matches (e.g. PSMs) with IDs for this feature More...
std::set< IdentificationData::ObservationMatchRef > &	getIDMatches ()
	mutable access to the set of matches (e.g. PSMs) with IDs for this feature More...
void	addIDMatch (IdentificationData::ObservationMatchRef ref)
	add an ID match (e.g. PSM) for this feature More...
void	updateIDReferences (const IdentificationData::RefTranslator &trans)
	Update ID references (primary ID, matches) for this feature. More...
Public Member Functions inherited from RichPeak2D
	RichPeak2D ()
	Default constructor. More...
	RichPeak2D (const RichPeak2D &p)=default
	Copy constructor. More...
	RichPeak2D (const Peak2D &p)
	Constructor from Peak2D. More...
	RichPeak2D (const PositionType &pos, const IntensityType in)
	Member constructor. More...
	RichPeak2D (RichPeak2D &&p)=default
	Move constructor. More...
	~RichPeak2D () override
	Destructor. More...
RichPeak2D &	operator= (const RichPeak2D &rhs)=default
	Assignment operator. More...
RichPeak2D &	operator= (RichPeak2D &&rhs) &=default
	Move Assignment operator. More...
RichPeak2D &	operator= (const Peak2D &rhs)
	Assignment operator. More...
bool	operator== (const RichPeak2D &rhs) const
	Equality operator. More...
bool	operator!= (const RichPeak2D &rhs) const
	Equality operator. More...
Public Member Functions inherited from Peak2D
bool	operator== (const Peak2D &rhs) const
	Equality operator. More...
bool	operator!= (const Peak2D &rhs) const
	Equality operator. More...
	Peak2D ()=default
	Peak2D (const PositionType &pos, const IntensityType in)
	Member constructor. More...
	Peak2D (const Peak2D &p)=default
	Copy constructor. More...
	Peak2D (Peak2D &&) noexcept=default
	Move constructor. More...
Peak2D &	operator= (const Peak2D &rhs)=default
	Assignment operator. More...
Peak2D &	operator= (Peak2D &&) noexcept=default
	Move assignment operator. More...
	~Peak2D () noexcept=default
	Destructor. More...
IntensityType	getIntensity () const
void	setIntensity (IntensityType intensity)
	Sets data point intensity (height) More...
PositionType const &	getPosition () const
	Non-mutable access to the position. More...
PositionType &	getPosition ()
	Mutable access to the position. More...
void	setPosition (const PositionType &position)
	Mutable access to the position. More...
CoordinateType	getMZ () const
	Returns the m/z coordinate (index 1) More...
void	setMZ (CoordinateType coordinate)
	Mutable access to the m/z coordinate (index 1) More...
CoordinateType	getRT () const
	Returns the RT coordinate (index 0) More...
void	setRT (CoordinateType coordinate)
	Mutable access to the RT coordinate (index 0) 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 Member Functions inherited from UniqueIdInterface
	UniqueIdInterface ()
	Default constructor - the unique id will be invalid More...
	UniqueIdInterface (const UniqueIdInterface &rhs)=default
	Copy constructor - copies the unique id. More...
	UniqueIdInterface (UniqueIdInterface &&rhs)=default
	Move constructor. More...
UniqueIdInterface &	operator= (UniqueIdInterface const &rhs)=default
	Assignment operator - copies the unique id. More...
UniqueIdInterface &	operator= (UniqueIdInterface &&) &=default
	Move Assignment operator - copies the unique id. More...
virtual	~UniqueIdInterface ()=default
	Destructor. More...
bool	operator== (UniqueIdInterface const &rhs) const
	Equality comparison operator - the unique ids must be equal (!) More...
UInt64	getUniqueId () const
	Non-mutable access to unique id - returns the unique id. More...
Size	clearUniqueId ()
	Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise. More...
void	swap (UniqueIdInterface &from)
Size	hasValidUniqueId () const
	Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise. More...
Size	hasInvalidUniqueId () const
	Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise. More...
Size	setUniqueId ()
	Assigns a new, valid unique id. Always returns 1. More...
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. More...
void	setUniqueId (UInt64 rhs)
	Assigns the given unique id. More...
void	setUniqueId (const String &rhs)
	Mutable access to unique id. More...

Model and quality methods
typedef QualityLess	OverallQualityLess
	Compare by quality. More...
QualityType	getOverallQuality () const
	Non-mutable access to the overall quality. More...
void	setOverallQuality (QualityType q)
	Set the overall quality. More...
QualityType	getQuality (Size index) const
	Non-mutable access to the quality in dimension c. More...
void	setQuality (Size index, QualityType q)
	Set the quality in dimension c. More...

Convex hulls and bounding box
QualityType	qualities_ [2]
	Quality measures for each dimension. More...
std::vector< ConvexHull2D >	convex_hulls_
	Array of convex hulls (one for each mass trace) More...
bool	convex_hulls_modified_ {}
	Flag that indicates if the overall convex hull needs to be recomputed (i.e. mass trace convex hulls were modified) More...
ConvexHull2D	convex_hull_
	Overall convex hull of the feature. More...
std::vector< Feature >	subordinates_
	subordinate features (e.g. features that represent alternative explanations, usually with lower quality) More...
const std::vector< ConvexHull2D > &	getConvexHulls () const
	Non-mutable access to the convex hulls. More...
std::vector< ConvexHull2D > &	getConvexHulls ()
	Mutable access to the convex hulls of single mass traces. More...
void	setConvexHulls (const std::vector< ConvexHull2D > &hulls)
	Set the convex hulls of single mass traces. More...
ConvexHull2D &	getConvexHull () const
	Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces) More...
bool	encloses (double rt, double mz) const
	Returns if the mass trace convex hulls of the feature enclose the position specified by rt and mz. More...
Feature &	operator= (const Feature &rhs)
	Assignment operator. More...
Feature &	operator= (Feature &&) &noexcept
	Move assignment operator. More...
bool	operator== (const Feature &rhs) const
	Equality operator. More...
const std::vector< Feature > &	getSubordinates () const
	immutable access to subordinate features More...
std::vector< Feature > &	getSubordinates ()
	mutable access to subordinate features More...
void	setSubordinates (const std::vector< Feature > &rhs)
	mutable access to subordinate features More...
template<typename Type >
Size	applyMemberFunction (Size(Type::*member_function)())
	Applies a member function of Type to the feature (including subordinates). The returned values are accumulated. More...
template<typename Type >
Size	applyMemberFunction (Size(Type::*member_function)() const) const
	The "const" variant. More...
void	updateAllIDReferences (const IdentificationData::RefTranslator &trans)
	Update ID references (primary ID, input matches) for this feature and any subfeatures. More...

Additional Inherited Members
Public Types inherited from BaseFeature
enum	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. More...
typedef float	WidthType
	Type of feature width/FWHM (RT) More...
Public Types inherited from Peak2D
typedef float	IntensityType
	Intensity type. More...
typedef double	CoordinateType
	Coordinate type (of the position) More...
typedef DPosition< 2 >	PositionType
	Position type. More...
enum	DimensionDescription { RT = 0 , MZ = 1 , DIMENSION = 2 }
	This enum maps the symbolic names of the dimensions to numbers. More...
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) More...
static char const *	shortDimensionNameRT ()
	Short name of the dimension (abbreviated form) More...
static char const *	shortDimensionNameMZ ()
	Short name of the dimension (abbreviated form) More...
static char const *	fullDimensionName (UInt const dim)
	Full name of the dimension (self-explanatory form) More...
static char const *	fullDimensionNameRT ()
	Full name of the dimension (self-explanatory form) More...
static char const *	fullDimensionNameMZ ()
	Full name of the dimension (self-explanatory form) More...
static char const *	shortDimensionUnit (UInt const dim)
	Unit of measurement (abbreviated form) More...
static char const *	shortDimensionUnitRT ()
	Unit of measurement (abbreviated form) More...
static char const *	shortDimensionUnitMZ ()
	Unit of measurement (abbreviated form) More...
static char const *	fullDimensionUnit (UInt const dim)
	Unit of measurement (self-explanatory form) More...
static char const *	fullDimensionUnitRT ()
	Unit of measurement (self-explanatory form) More...
static char const *	fullDimensionUnitMZ ()
	Unit of measurement (self-explanatory form) More...
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...
Static Public Member Functions inherited from UniqueIdInterface
static bool	isValid (UInt64 unique_id)
	Returns true if the unique_id is valid, false otherwise. More...
Static Public Attributes inherited from BaseFeature
static const std::string	NamesOfAnnotationState [SIZE_OF_ANNOTATIONSTATE]
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...
Protected Attributes inherited from BaseFeature
QualityType	quality_
	Overall quality measure of the feature. More...
ChargeType	charge_
	Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state. More...
WidthType	width_
	Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model. More...
std::vector< PeptideIdentification >	peptides_
	PeptideIdentifications belonging to the feature. More...
std::optional< IdentificationData::IdentifiedMolecule >	primary_id_
	primary ID (peptide, RNA, compound) assigned to this feature More...
std::set< IdentificationData::ObservationMatchRef >	id_matches_
	set of observation matches (e.g. PSMs) with IDs for this feature More...
Protected Attributes inherited from Peak2D
PositionType	position_ {}
	The data point position. More...
IntensityType	intensity_ {}
	The data point intensity. More...
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...
Protected Attributes inherited from UniqueIdInterface
UInt64	unique_id_
	the unique id More...
Static Protected Attributes inherited from Peak2D
static char const *const	dimension_name_short_ [DIMENSION]
	Short name of the dimension (abbreviated form) More...
static char const *const	dimension_name_full_ [DIMENSION]
	Full name of the dimension (self-explanatory form) More...
static char const *const	dimension_unit_short_ [DIMENSION]
	Unit of measurement (abbreviated form) More...
static char const *const	dimension_unit_full_ [DIMENSION]
	Unit of measurement (self-explanatory form) More...

Detailed Description

An LC-MS feature.

The Feature class is used to describe the two-dimensional signal caused by an analyte. It can store a charge state and a list of peptide identifications (for peptides). The area occupied by the Feature in the LC-MS data set is represented by a list of convex hulls (one for each isotopic peak). There is also a convex hull for the entire Feature. The model description can store the parameters of a two-dimensional theoretical model of the underlying signal in LC-MS. Currently, non-peptide compounds are also represented as features.

By convention in OpenMS, the position of a feature is defined as maximum position of the model for the retention time dimension and the mass of the monoisotopic peak for the m/z dimension. The intensity of a feature is (proportional to) its total ion count.

Feature is derived from RichPeak2D. Also inherited is a MetaInfoInterface. Features as usually are contained in a FeatureMap. See also FeatureHandle and ConsensusFeature.

Member Typedef Documentation

OverallQualityLess

typedef QualityLess OverallQualityLess

Compare by quality.

Constructor & Destructor Documentation

Feature() [1/4]

Feature

(

)

Default constructor.

Feature() [2/4]

Feature ( const BaseFeature &  base )

explicit

explicit C'tor from BaseFeature

Feature() [3/4]

Feature

(

const Feature &

feature

)

Copy constructor.

Feature() [4/4]

Feature ( Feature &&  )

noexcept

Move constructor.

~Feature()

~Feature ( )

override

Destructor.

Member Function Documentation

applyMemberFunction() [1/2]

Size applyMemberFunction ( Size(Type::*)() const  member_function ) const

inline

The "const" variant.

applyMemberFunction() [2/2]

Size applyMemberFunction ( Size(Type::*)()  member_function )

inline

Applies a member function of Type to the feature (including subordinates). The returned values are accumulated.

Example: The following will print the number of features (parent feature and subordinates) with invalid unique ids:

Feature f;
(...)
std::cout << f.applyMemberFunction(&UniqueIdInterface::hasInvalidUniqueId) << std::endl;

See e.g. UniqueIdInterface for what else can be done this way.

References Feature::applyMemberFunction().

Referenced by Feature::applyMemberFunction().

encloses()

bool encloses	(	double	rt,
		double	mz
	)		const

Returns if the mass trace convex hulls of the feature enclose the position specified by rt and mz.

getConvexHull()

ConvexHull2D& getConvexHull

(

)

const

Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces)

Note

the bounding box of the feature can be accessed through the returned convex hull

getConvexHulls() [1/2]

std::vector<ConvexHull2D>& getConvexHulls

(

)

Mutable access to the convex hulls of single mass traces.

getConvexHulls() [2/2]

const std::vector<ConvexHull2D>& getConvexHulls

(

)

const

Non-mutable access to the convex hulls.

Referenced by EmgScoring::calcElutionFitScore(), MRMTransitionGroupPicker::pickFragmentChromatograms(), and MRMTransitionGroupPicker::pickPrecursorChromatograms().

getOverallQuality()

QualityType getOverallQuality

(

)

const

Non-mutable access to the overall quality.

Referenced by FeatureOverlapFilter::filter(), and FeatureFinderIdentificationAlgorithm::FeatureFilterQuality::operator()().

getQuality()

QualityType getQuality

(

Size

index

)

const

Non-mutable access to the quality in dimension c.

getSubordinates() [1/2]

std::vector<Feature>& getSubordinates

(

)

mutable access to subordinate features

getSubordinates() [2/2]

const std::vector<Feature>& getSubordinates

(

)

const

immutable access to subordinate features

operator=() [1/2]

Feature& operator=

(

const Feature &

rhs

)

Assignment operator.

operator=() [2/2]

Feature& operator= ( Feature &&  ) &

noexcept

Move assignment operator.

operator==()

bool operator==

(

const Feature &

rhs

)

const

Equality operator.

setConvexHulls()

void setConvexHulls

(

const std::vector< ConvexHull2D > &

hulls

)

Set the convex hulls of single mass traces.

setOverallQuality()

void setOverallQuality

(

QualityType

q

)

Set the overall quality.

Referenced by MRMTransitionGroupPicker::createMRMFeature(), MsInspectFile::load(), MRMTransitionGroupPicker::pickFragmentChromatograms(), and MRMTransitionGroupPicker::pickPrecursorChromatograms().

setQuality()

void setQuality	(	Size	index,
		QualityType	q
	)

Set the quality in dimension c.

Referenced by MRMTransitionGroupPicker::pickFragmentChromatograms(), and MRMTransitionGroupPicker::pickPrecursorChromatograms().

setSubordinates()

void setSubordinates

(

const std::vector< Feature > &

rhs

)

mutable access to subordinate features

updateAllIDReferences()

void updateAllIDReferences

(

const IdentificationData::RefTranslator &

trans

)

Update ID references (primary ID, input matches) for this feature and any subfeatures.

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

Member Data Documentation

convex_hull_

ConvexHull2D convex_hull_

mutableprotected

Overall convex hull of the feature.

convex_hulls_

std::vector<ConvexHull2D> convex_hulls_

protected

Array of convex hulls (one for each mass trace)

convex_hulls_modified_

bool convex_hulls_modified_ {}

mutableprotected

Flag that indicates if the overall convex hull needs to be recomputed (i.e. mass trace convex hulls were modified)

qualities_

QualityType qualities_[2]

protected

Quality measures for each dimension.

subordinates_

std::vector<Feature> subordinates_

protected

subordinate features (e.g. features that represent alternative explanations, usually with lower quality)