A consensus feature spanning multiple LC-MS/MS experiments. More...

#include <OpenMS/KERNEL/ConsensusFeature.h>

Inheritance diagram for ConsensusFeature:

Collaboration diagram for ConsensusFeature:

Classes
struct	MapsLess
	Compare by the sets of consensus elements (lexicographically) More...

struct	Ratio
	slim struct to feed the need for systematically storing of ratios ( More...

struct	SizeLess
	Compare by size(), the number of consensus elements. More...

Public Types
typedef std::set< FeatureHandle, FeatureHandle::IndexLess >	HandleSetType
	Type definitions. More...

typedef HandleSetType::const_iterator	const_iterator

typedef HandleSetType::iterator	iterator

typedef HandleSetType::const_reverse_iterator	const_reverse_iterator

typedef HandleSetType::reverse_iterator	reverse_iterator

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 getIDState() to query it More...

typedef float	QualityType
	Type of quality values. More...

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...

Public Member Functions
Constructors and Destructor
	ConsensusFeature ()
	Default constructor. More...

	ConsensusFeature (const ConsensusFeature &rhs)=default
	Copy constructor. More...

	ConsensusFeature (ConsensusFeature &&rhs)=default
	Move constructor. More...

	ConsensusFeature (const BaseFeature &feature)
	Constructor from basic feature. More...

	ConsensusFeature (UInt64 map_index, const Peak2D &element, UInt64 element_index)
	Constructor with map and element index for a singleton consensus feature. More...

	ConsensusFeature (UInt64 map_index, const BaseFeature &element)
	Constructor with map index for a singleton consensus feature. More...

ConsensusFeature &	operator= (const ConsensusFeature &rhs)=default
	Assignment operator. More...

ConsensusFeature &	operator= (ConsensusFeature &&rhs)=default
	Move Assignment operator. More...

	~ConsensusFeature () override
	Destructor. More...

Management of feature handles
void	insert (const ConsensusFeature &cf)
	Adds all feature handles (of the CF) into the consensus feature. More...

void	insert (const FeatureHandle &handle)
	Adds an feature handle into the consensus feature. More...

void	insert (const HandleSetType &handle_set)
	Adds all feature handles in `handle_set` to this consensus feature. More...

void	insert (UInt64 map_index, const Peak2D &element, UInt64 element_index)
	Creates a FeatureHandle and adds it. More...

void	insert (UInt64 map_index, const BaseFeature &element)
	Creates a FeatureHandle and adds it. More...

const HandleSetType &	getFeatures () const
	Non-mutable access to the contained feature handles. More...

std::vector< FeatureHandle >	getFeatureList () const
	Mutable access to a copy of the contained feature handles. More...

void	setFeatures (HandleSetType h)
	Set the feature set to a new one. More...

Accessors
DRange< 2 >	getPositionRange () const
	Returns the position range of the contained elements. More...

DRange< 1 >	getIntensityRange () const
	Returns the intensity range of the contained elements. More...

void	computeConsensus ()
	Computes and updates the consensus position, intensity, and charge. More...

void	computeMonoisotopicConsensus ()
	Computes and updates the consensus position, intensity, and charge. More...

void	computeDechargeConsensus (const FeatureMap &fm, bool intensity_weighted_averaging=false)
	Computes the uncharged parent RT & mass, assuming the handles are charge variants. More...

void	addRatio (const Ratio &r)
	Add a ratio. More...

void	setRatios (std::vector< Ratio > &rs)
	Add a ratio vector. More...

std::vector< Ratio >	getRatios () const
	Get the ratio vector. More...

std::vector< Ratio > &	getRatios ()
	Get the ratio vector. More...

Public Member Functions inherited from BaseFeature
	BaseFeature ()
	Default constructor. More...

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

	BaseFeature (BaseFeature &&feature)=default
	Move constructor. More...

	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
	Non-mutable access to the overall quality. More...

void	setQuality (QualityType q)
	Set the overall quality. More...

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...

const std::vector< PeptideIdentification > &	getPeptideIdentifications () const
	returns a const reference to the PeptideIdentification vector More...

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...

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...

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

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

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

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

	Peak2D ()

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

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

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

	~Peak2D ()
	Destructor. More...

IntensityType	getIntensity () const

void	setIntensity (IntensityType intensity)
	Non-mutable access to the 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...

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 DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...

const DataValue &	getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to an index, or a default value (default: 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...

Accessors for set of FeatureHandles
HandleSetType	handles_

std::vector< Ratio >	ratios_

Size	size () const

const_iterator	begin () const

iterator	begin ()

const_iterator	end () const

iterator	end ()

const_reverse_iterator	rbegin () const

reverse_iterator	rbegin ()

const_reverse_iterator	rend () const

reverse_iterator	rend ()

void	clear ()

bool	empty () const

Additional Inherited Members
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...

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

A consensus feature spanning multiple LC-MS/MS experiments.

A ConsensusFeature represents analytes that have been quantified across multiple LC-MS/MS experiments. Each analyte in a ConsensusFeature is linked to its original LC-MS/MS run through a unique identifier.

A consensus feature represents corresponding features in multiple feature maps. The corresponding features are represented a set of FeatureHandle instances. Each ConsensusFeature "contains" zero or more FeatureHandles.

See also: ConsensusMap

Member Typedef Documentation

◆ const_iterator

typedef HandleSetType::const_iterator const_iterator

◆ const_reverse_iterator

typedef HandleSetType::const_reverse_iterator const_reverse_iterator

◆ HandleSetType

typedef std::set<FeatureHandle, FeatureHandle::IndexLess> HandleSetType

Type definitions.

◆ iterator

typedef HandleSetType::iterator iterator

◆ reverse_iterator

typedef HandleSetType::reverse_iterator reverse_iterator

Constructor & Destructor Documentation

◆ ConsensusFeature() [1/6]

ConsensusFeature ( )

Default constructor.

◆ ConsensusFeature() [2/6]

ConsensusFeature ( const ConsensusFeature & rhs )

default

Copy constructor.

◆ ConsensusFeature() [3/6]

ConsensusFeature ( ConsensusFeature && rhs )

default

Move constructor.

◆ ConsensusFeature() [4/6]

ConsensusFeature ( const BaseFeature & feature )

explicit

Constructor from basic feature.

◆ ConsensusFeature() [5/6]

ConsensusFeature	(	UInt64	map_index,
		const Peak2D &	element,
		UInt64	element_index
	)

Constructor with map and element index for a singleton consensus feature.

Sets the consensus feature position and intensity to the values of element as well.

◆ ConsensusFeature() [6/6]

ConsensusFeature	(	UInt64	map_index,
		const BaseFeature &	element
	)

Constructor with map index for a singleton consensus feature.

Sets the consensus feature position, intensity, charge, quality, and peptide identifications to the values of element as well.

◆ ~ConsensusFeature()

~ConsensusFeature ( )

override

Destructor.

Member Function Documentation

◆ addRatio()

void addRatio ( const Ratio & r )

Add a ratio.

Connects a ratio to the ConsensusFeature.

Note: still experimental. consensusfeaturehandler will ignore it.

◆ begin() [1/2]

iterator begin ( )

◆ begin() [2/2]

const_iterator begin ( ) const

Referenced by TOPPGNPSExport::main_(), ConsensusFeature::MapsLess::operator()(), and TOPPGNPSExport::sortElementMapsByIntensity_().

◆ clear()

void clear ( )

◆ computeConsensus()

void computeConsensus ( )

Computes and updates the consensus position, intensity, and charge.

The position and intensity of the contained feature handles is averaged. The most frequent charge state wins, while the tie breaking prefers smaller (absolute) charges.

Note: This method has to be called explicitly, after adding the feature handles.

◆ computeDechargeConsensus()

void computeDechargeConsensus	(	const FeatureMap &	fm,
		bool	intensity_weighted_averaging = `false`
	)

Computes the uncharged parent RT & mass, assuming the handles are charge variants.

The position of the feature handles (decharged) is averaged (using intensity as weights if intensity_weighted_averaging is true). Intensities are summed up. Charge is set to 0. Mass calculation: If the given features contain a metavalue "dc_charge_adduct_mass" then this will be used as adduct mass instead of weight(H+) * charge.

Note: This method has to be called explicitly, after adding the feature handles.

Parameters

fm	Input feature map, which provides additional information on the features
intensity_weighted_averaging	Use unweighted averaging (default) or weighted by intensity

◆ computeMonoisotopicConsensus()

void computeMonoisotopicConsensus ( )

Computes and updates the consensus position, intensity, and charge.

The m/z position is the lowest m/z value of the feature handles. The RT position and intensity of the contained feature handles is averaged. The most frequent charge state wins, while the tie breaking prefers smaller (absolute) charges.

Note: This method has to be called explicitly, after adding the feature handles.

◆ empty()

bool empty ( ) const

◆ end() [1/2]

iterator end ( )

◆ end() [2/2]

const_iterator end ( ) const

Referenced by TOPPGNPSExport::main_(), ConsensusFeature::MapsLess::operator()(), and TOPPGNPSExport::sortElementMapsByIntensity_().

◆ getFeatureList()

std::vector<FeatureHandle> getFeatureList ( ) const

Mutable access to a copy of the contained feature handles.

◆ getFeatures()

const HandleSetType& getFeatures ( ) const

Non-mutable access to the contained feature handles.

◆ getIntensityRange()

DRange<1> getIntensityRange ( ) const

Returns the intensity range of the contained elements.

◆ getPositionRange()

DRange<2> getPositionRange ( ) const

Returns the position range of the contained elements.

◆ getRatios() [1/2]

std::vector<Ratio>& getRatios ( )

Get the ratio vector.

◆ getRatios() [2/2]

std::vector<Ratio> getRatios ( ) const

Get the ratio vector.

◆ insert() [1/5]

void insert ( const ConsensusFeature & cf )

Adds all feature handles (of the CF) into the consensus feature.

◆ insert() [2/5]

void insert ( const FeatureHandle & handle )

Adds an feature handle into the consensus feature.

Exceptions

Exception::InvalidValue is thrown if a handle with the same map index and unique id already exists.

◆ insert() [3/5]

void insert ( const HandleSetType & handle_set )

Adds all feature handles in handle_set to this consensus feature.

◆ insert() [4/5]

void insert	(	UInt64	map_index,
		const BaseFeature &	element
	)

Creates a FeatureHandle and adds it.

Exceptions

Exception::InvalidValue is thrown if a handle with the same map index and unique id already exists.

◆ insert() [5/5]

void insert	(	UInt64	map_index,
		const Peak2D &	element,
		UInt64	element_index
	)

Creates a FeatureHandle and adds it.

Exceptions

Exception::InvalidValue is thrown if a handle with the same map index and unique id already exists.

◆ operator=() [1/2]

ConsensusFeature& operator= ( ConsensusFeature && rhs )

default

Move Assignment operator.

◆ operator=() [2/2]

ConsensusFeature& operator= ( const ConsensusFeature & rhs )

default

Assignment operator.

◆ rbegin() [1/2]

reverse_iterator rbegin ( )

◆ rbegin() [2/2]

const_reverse_iterator rbegin ( ) const

◆ rend() [1/2]

reverse_iterator rend ( )

◆ rend() [2/2]

const_reverse_iterator rend ( ) const

◆ setFeatures()

void setFeatures ( HandleSetType h )

Set the feature set to a new one.

◆ setRatios()

void setRatios ( std::vector< Ratio > & rs )

Add a ratio vector.

Connects the ratios to the ConsensusFeature.

Note: still experimental. consensusfeaturehandler will ignore it.

◆ size()

Size size ( ) const

Referenced by ConsensusFeature::SizeLess::operator()().

Member Data Documentation

◆ handles_

HandleSetType handles_

private

◆ ratios_

std::vector<Ratio> ratios_

private

Classes

Public Types

Public Member Functions

Accessors for set of FeatureHandles

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ const_reverse_iterator

◆ HandleSetType

◆ iterator

◆ reverse_iterator

Constructor & Destructor Documentation

◆ ConsensusFeature() [1/6]

◆ ConsensusFeature() [2/6]

◆ ConsensusFeature() [3/6]

◆ ConsensusFeature() [4/6]

◆ ConsensusFeature() [5/6]

◆ ConsensusFeature() [6/6]

◆ ~ConsensusFeature()

Member Function Documentation

◆ addRatio()

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ computeConsensus()

◆ computeDechargeConsensus()

◆ computeMonoisotopicConsensus()

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ getFeatureList()

◆ getFeatures()

◆ getIntensityRange()

◆ getPositionRange()

◆ getRatios() [1/2]

◆ getRatios() [2/2]

◆ insert() [1/5]

◆ insert() [2/5]

◆ insert() [3/5]

◆ insert() [4/5]

◆ insert() [5/5]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ rbegin() [1/2]

◆ rbegin() [2/2]

◆ rend() [1/2]

◆ rend() [2/2]

◆ setFeatures()

◆ setRatios()

◆ size()

Member Data Documentation

◆ handles_

◆ ratios_