MRMFeature Class Reference

A multi-chromatogram MRM feature. More...

#include <OpenMS/KERNEL/MRMFeature.h>

Inheritance diagram for MRMFeature:

Collaboration diagram for MRMFeature:

Public Types
typedef std::vector< Feature >	FeatureListType
	Type definitions.
Public Types inherited from Feature
typedef QualityLess	OverallQualityLess
	Compare by quality.
Public Types inherited from BaseFeature
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)
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...

Public Member Functions
Constructors and Destructor
	MRMFeature ()
	Default constructor.
	MRMFeature (const MRMFeature &rhs)
	Copy constructor.
	MRMFeature (MRMFeature &&rhs)=default
	Move constructor.
MRMFeature &	operator= (const MRMFeature &rhs)
	Assignment operator.
MRMFeature &	operator= (MRMFeature &&) &=default
	Move assignment operator.
	~MRMFeature () override
	Destructor.
Public Member Functions inherited from Feature
	Feature ()
	Default constructor.
	Feature (const BaseFeature &base)
	explicit C'tor from BaseFeature
	Feature (const Feature &feature)
	Copy constructor.
	Feature (Feature &&) noexcept
	Move constructor.
	~Feature () override
	Destructor.
QualityType	getOverallQuality () const
	Non-mutable access to the overall quality.
void	setOverallQuality (QualityType q)
	Set the overall quality.
QualityType	getQuality (Size index) const
	Non-mutable access to the quality in dimension c.
void	setQuality (Size index, QualityType q)
	Set the quality in dimension c.
const std::vector< ConvexHull2D > &	getConvexHulls () const
	Non-mutable access to the convex hulls.
std::vector< ConvexHull2D > &	getConvexHulls ()
	Mutable access to the convex hulls of single mass traces.
void	setConvexHulls (const std::vector< ConvexHull2D > &hulls)
	Set the convex hulls of single mass traces.
ConvexHull2D &	getConvexHull () const
	Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces)
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.
Feature &	operator= (const Feature &rhs)
	Assignment operator.
Feature &	operator= (Feature &&) &noexcept
	Move assignment operator.
bool	operator== (const Feature &rhs) const
	Equality operator.
const std::vector< Feature > &	getSubordinates () const
	immutable access to subordinate features
std::vector< Feature > &	getSubordinates ()
	mutable access to subordinate features
void	setSubordinates (const std::vector< Feature > &rhs)
	mutable access to subordinate features
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.
template<typename Type >
Size	applyMemberFunction (Size(Type::*member_function)() const) const
	The "const" variant.
void	updateAllIDReferences (const IdentificationData::RefTranslator &trans)
	Update ID references (primary ID, input matches) for this feature and any subfeatures.
Public Member Functions inherited from BaseFeature
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
	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.
QualityType	getQuality () const
void	setQuality (QualityType q)
	Set the overall quality.
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 PeptideIdentifications, assuming they have the same scoreType.
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.

Accessors
FeatureListType	features_
FeatureListType	precursor_features_
OpenSwath_Scores	pg_scores_
	peak group scores
std::map< std::string, int >	feature_map_
	map native ids to the features
std::map< std::string, int >	precursor_feature_map_
	map native ids to the precursor features
const OpenSwath_Scores &	getScores () const
	get all peakgroup scores
OpenSwath_Scores &	getScores ()
	get all peakgroup scores
Feature &	getFeature (const std::string &key)
	get a specified feature
const Feature &	getFeature (const std::string &key) const
	get a specified feature (const)
void	setScores (const OpenSwath_Scores &scores)
	set all peakgroup scores
void	addScore (const std::string &score_name, double score)
	set a single peakgroup score
void	addFeature (const Feature &feature, const std::string &key)
	Adds an feature from a single chromatogram into the feature.
void	addFeature (Feature &&feature, const std::string &key)
const std::vector< Feature > &	getFeatures () const
	get a list of features
void	getFeatureIDs (std::vector< std::string > &result) const
	get a list of IDs of available features
void	addPrecursorFeature (const Feature &feature, const std::string &key)
	Adds a precursor feature from a single chromatogram into the feature.
void	addPrecursorFeature (Feature &&feature, const std::string &key)
void	getPrecursorFeatureIDs (std::vector< std::string > &result) const
	get a list of IDs of available precursor features
Feature &	getPrecursorFeature (const std::string &key)
	get a specified precursor feature
const Feature &	getPrecursorFeature (const std::string &key) const
	get a specified precursor feature (const)
void	IDScoresAsMetaValue (bool decoy, const OpenSwath_Ind_Scores &idscores)

Additional Inherited Members
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.
Static Public Attributes inherited from BaseFeature
static const std::string	NamesOfAnnotationState [static_cast< size_t >(AnnotationState::SIZE_OF_ANNOTATIONSTATE)]
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.
Protected Attributes inherited from Feature
QualityType	qualities_ [2]
	Quality measures for each dimension.
std::vector< ConvexHull2D >	convex_hulls_
	Array of convex hulls (one for each mass trace)
bool	convex_hulls_modified_ {}
	Flag that indicates if the overall convex hull needs to be recomputed (i.e. mass trace convex hulls were modified)
ConvexHull2D	convex_hull_
	Overall convex hull of the feature.
std::vector< Feature >	subordinates_
	subordinate features (e.g. features that represent alternative explanations, usually with lower quality)
Protected Attributes inherited from BaseFeature
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
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 multi-chromatogram MRM feature.

An MRM feature contains corresponding features in multiple chromatograms, it is thus a representation of a peak group. The individual features in each chromatogram are represented by OpenMS Features.

Member Typedef Documentation

FeatureListType

typedef std::vector<Feature> FeatureListType

Type definitions.

Feature list type

Constructor & Destructor Documentation

MRMFeature() [1/3]

MRMFeature

(

)

Default constructor.

MRMFeature() [2/3]

MRMFeature

(

const MRMFeature &

rhs

)

Copy constructor.

MRMFeature() [3/3]

MRMFeature ( MRMFeature &&  rhs )

default

Move constructor.

~MRMFeature()

~MRMFeature ( )

override

Destructor.

Member Function Documentation

addFeature() [1/2]

void addFeature	(	const Feature &	feature,
		const std::string &	key
	)

Adds an feature from a single chromatogram into the feature.

Referenced by MRMTransitionGroupPicker::pickFragmentChromatograms(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subset().

addFeature() [2/2]

void addFeature	(	Feature &&	feature,
		const std::string &	key
	)

addPrecursorFeature() [1/2]

void addPrecursorFeature	(	const Feature &	feature,
		const std::string &	key
	)

Adds a precursor feature from a single chromatogram into the feature.

Referenced by MRMTransitionGroupPicker::pickPrecursorChromatograms(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subset().

addPrecursorFeature() [2/2]

void addPrecursorFeature	(	Feature &&	feature,
		const std::string &	key
	)

addScore()

void addScore	(	const std::string &	score_name,
		double	score
	)

set a single peakgroup score

getFeature() [1/2]

Feature & getFeature

(

const std::string &

key

)

get a specified feature

Referenced by EmgScoring::calcElutionFitScore().

getFeature() [2/2]

const Feature & getFeature

(

const std::string &

key

)

const

get a specified feature (const)

getFeatureIDs()

void getFeatureIDs

(

std::vector< std::string > &

result

)

const

get a list of IDs of available features

getFeatures()

const std::vector< Feature > & getFeatures

(

)

const

get a list of features

getPrecursorFeature() [1/2]

Feature & getPrecursorFeature

(

const std::string &

key

)

get a specified precursor feature

getPrecursorFeature() [2/2]

const Feature & getPrecursorFeature

(

const std::string &

key

)

const

get a specified precursor feature (const)

getPrecursorFeatureIDs()

void getPrecursorFeatureIDs

(

std::vector< std::string > &

result

)

const

get a list of IDs of available precursor features

getScores() [1/2]

OpenSwath_Scores & getScores

(

)

get all peakgroup scores

getScores() [2/2]

const OpenSwath_Scores & getScores

(

)

const

get all peakgroup scores

IDScoresAsMetaValue()

void IDScoresAsMetaValue	(	bool	decoy,
		const OpenSwath_Ind_Scores &	idscores
	)

operator=() [1/2]

MRMFeature & operator=

(

const MRMFeature &

rhs

)

Assignment operator.

operator=() [2/2]

MRMFeature & operator= ( MRMFeature &&  ) &

default

Move assignment operator.

setScores()

void setScores

(

const OpenSwath_Scores &

scores

)

set all peakgroup scores

Member Data Documentation

feature_map_

std::map<std::string, int> feature_map_

protected

map native ids to the features

features_

FeatureListType features_

protected

pg_scores_

OpenSwath_Scores pg_scores_

protected

peak group scores

precursor_feature_map_

std::map<std::string, int> precursor_feature_map_

protected

map native ids to the precursor features

precursor_features_

FeatureListType precursor_features_

protected