An LC-MS feature. More...

#include <OpenMS/KERNEL/Feature.h>

Inheritance diagram for Feature:

Public Member Functions
Feature &	operator= (const Feature &rhs)
	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.
Constructors and Destructor

	Feature ()
	Default constructor.
	Feature (const Feature &feature)
	Copy constructor.
	~Feature ()
	Destructor.
Convex hulls and bounding box

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 (DoubleReal rt, DoubleReal mz) const
	Returns if the mass trace convex hulls of the feature enclose the position specified by `rt` and `mz`.
Protected Attributes
QualityType	qualities_ [2]
	Quality measures for each dimension.
ModelDescription< 2 >	model_desc_
	Description of the theoretical model the feature was constructed with.
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 the ModelFitter discarded due to inferior quality)
Model and quality methods

typedef QualityLess	OverallQualityLess
	Compare by quality.
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 ModelDescription< 2 > &	getModelDescription () const
	Non-mutable access to the model description.
ModelDescription< 2 > &	getModelDescription ()
	Mutable access to the model description.
void	setModelDescription (const ModelDescription< 2 > &q)
	Set the model description.

Detailed Description

An LC-MS feature.

The Feature class is used to describe the two-dimensional signal caused by a peptide. It can store a charge state and a list of peptide identifications. 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-peptidic 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

typedef QualityLess OverallQualityLess

Compare by quality.

Constructor & Destructor Documentation

Feature ( )

Default constructor.

Feature ( const Feature & feature )

Copy constructor.

~Feature ( )

Destructor.

Member Function Documentation

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.

Size applyMemberFunction ( Size(Type::*)() const member_function ) const [inline]

The "const" variant.

bool encloses	(	DoubleReal	rt,
		DoubleReal	mz
	)			const

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

Referenced by ModelFitter< PeakType, FeatureType >::fit(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

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

Referenced by ModelFitter< PeakType, FeatureType >::fit(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

const std::vector<ConvexHull2D>& getConvexHulls ( ) const

Non-mutable access to the convex hulls.

Referenced by FeaFiModule< PeakType, FeatureType >::addConvexHull(), IDMapper::annotate(), EmgScoring::calcElutionFitScore(), MRMTransitionGroupPicker::createMRMFeature(), OpenMS::enclosesBoundingBox(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intersection_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

std::vector<ConvexHull2D>& getConvexHulls ( )

Mutable access to the convex hulls of single mass traces.

const ModelDescription<2>& getModelDescription ( ) const

Non-mutable access to the model description.

Referenced by ModelFitter< PeakType, FeatureType >::fit(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run().

ModelDescription<2>& getModelDescription ( )

Mutable access to the model description.

QualityType getOverallQuality ( ) const

Non-mutable access to the overall quality.

Referenced by ModelFitter< PeakType, FeatureType >::fit(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

QualityType getQuality ( Size index ) const

Non-mutable access to the quality in dimension c.

Referenced by ModelFitter< PeakType, FeatureType >::fit().

std::vector<Feature>& getSubordinates ( )

mutable access to subordinate features

const std::vector<Feature>& getSubordinates ( ) const

immutable access to subordinate features

Referenced by ModelFitter< PeakType, FeatureType >::fit(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

Feature& operator= ( const Feature & rhs )

Assignment operator.

bool operator== ( const Feature & rhs ) const

Equality operator.

void setConvexHulls ( const std::vector< ConvexHull2D > & hulls )

Set the convex hulls of single mass traces.

Referenced by KroenikFile::load(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().

void setModelDescription ( const ModelDescription< 2 > & q )

Set the model description.

Referenced by ModelFitter< PeakType, FeatureType >::fit(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

void setOverallQuality ( QualityType q )

Set the overall quality.

Referenced by MRMFeatureFinderScoring::calculateSwathScores_(), MRMTransitionGroupPicker::createMRMFeature(), ModelFitter< PeakType, FeatureType >::fit(), MsInspectFile::load(), KroenikFile::load(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

void setQuality	(	Size	index,
		QualityType	q
	)

Set the quality in dimension c.

Referenced by MRMTransitionGroupPicker::createMRMFeature(), ModelFitter< PeakType, FeatureType >::fit(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

void setSubordinates ( const std::vector< Feature > & rhs )

mutable access to subordinate features

Member Data Documentation

ConvexHull2D convex_hull_ [mutable, protected]

Overall convex hull of the feature.

std::vector<ConvexHull2D> convex_hulls_ [protected]

Array of convex hulls (one for each mass trace).

bool convex_hulls_modified_ [mutable, protected]

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

ModelDescription<2> model_desc_ [protected]

Description of the theoretical model the feature was constructed with.

QualityType qualities_[2] [protected]

Quality measures for each dimension.

std::vector<Feature> subordinates_ [protected]

subordinate features (e.g. features that the ModelFitter discarded due to inferior quality)

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1

Feature Class Reference [Kernel]

Public Member Functions

Protected Attributes

Model and quality methods

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

Feature Class Reference
[Kernel]