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Feature Class Reference
[Kernel]

#include <OpenMS/KERNEL/Feature.h>

Inheritance diagram for Feature:

Peak2D RawDataPoint2D MetaInfoInterface ConsensusFeature

List of all members.


Detailed Description

A feature.

A feature represents a subset of peaks in a map. In general, it summarizes all peaks related to a specific peptide or chemical compound and thus reduces partitions of the LCMS dataset to a more meaningful entity. Picked peaks and raw data points can be converted to features through the FeatureFinder.

Features are usually contained in FeatureMap. Features themselves can either contain features again (composite design pattern) or their constituent peaks.

Hierarchical relationships in features (i.e. features containing features containing features...) can be used to express group relationships. For example, one might group the features corresponding to an ICAT pair into an aggregate ICAT feature.

Features are derived from DPeak, as they inherit most of their properties. In particular, a feature has a position and an intensity. 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.

Public Types

Type definitions
enum  { DIMENSION = 2 }
 Dimensionality of the feature. More...
typedef DoubleReal QualityType
 Type of the quality values.
typedef Int ChargeType
 Charge type.

Public Member Functions

const ChargeTypegetCharge () const
 Non-mutable access to charge state.
void setCharge (const ChargeType &ch)
 Set charge state.
Featureoperator= (const Feature &rhs)
 Assignment operator.
bool operator== (const Feature &rhs) const
 Equality operator.
const std::vector
< PeptideIdentification > & 
getPeptideIdentifications () const
 returns a const reference to the PeptideIdentification vector
std::vector
< PeptideIdentification > & 
getPeptideIdentifications ()
 returns a mutable reference to the PeptideIdentification vector
void setPeptideIdentifications (const std::vector< PeptideIdentification > &identifications)
 sets the PeptideIdentification vector
Constructors and Destructor
 Feature ()
 Default constructor.
 Feature (const Feature &feature)
 Copy constructor.
 ~Feature ()
 Destructor.
Model and Quality methods
QualityType getOverallQuality () const
 Non-mutable access to the overall quality.
void setOverallQuality (QualityType q)
 Set the overall quality.
QualityType getQuality (UInt index) const
 Non-mutable access to the quality in dimension c.
void setQuality (UInt 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.
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.
ConvexHull2DgetConvexHull () 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 overall_quality_
 Overall quality measure of the feature.
QualityType qualities_ [2]
 Quality measures for each dimension.
ModelDescription< 2 > model_desc_
 Description of the theoretical model the feature was constructed with.
std::vector< ConvexHull2Dconvex_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.
ChargeType charge_
 Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state.
std::vector
< PeptideIdentification
identifications_
 Peptide PeptideIdentifications belonging to the feature.

Classes

struct  OverallQualityLess
 Compare by getOverallQuality(). More...


Member Typedef Documentation

typedef DoubleReal QualityType

Type of the quality values.

typedef Int ChargeType

Charge type.


Member Enumeration Documentation

anonymous enum

Dimensionality of the feature.

Enumerator:
DIMENSION  Number of dimensions.


Constructor & Destructor Documentation

Feature (  )  [inline]

Default constructor.

Feature ( const Feature feature  )  [inline]

Copy constructor.

~Feature (  )  [inline]

Destructor.


Member Function Documentation

QualityType getOverallQuality (  )  const [inline]

Non-mutable access to the overall quality.

void setOverallQuality ( QualityType  q  )  [inline]

Set the overall quality.

QualityType getQuality ( UInt  index  )  const [inline]

Non-mutable access to the quality in dimension c.

void setQuality ( UInt  index,
QualityType  q 
) [inline]

Set the quality in dimension c.

const ModelDescription<2>& getModelDescription (  )  const [inline]

Non-mutable access to the model description.

ModelDescription<2>& getModelDescription (  )  [inline]

Mutable access to the model description.

void setModelDescription ( const ModelDescription< 2 > &  q  )  [inline]

Set the model description.

const ChargeType& getCharge (  )  const [inline]

Non-mutable access to charge state.

void setCharge ( const ChargeType ch  )  [inline]

Set charge state.

const std::vector<ConvexHull2D>& getConvexHulls (  )  const [inline]

Non-mutable access to the convex hulls.

std::vector<ConvexHull2D>& getConvexHulls (  )  [inline]

Mutable access to the convex hulls of single mass traces.

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

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).

Note:
the bounding boy of the feature can be accessed through the returned convex hull

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.

Feature& operator= ( const Feature rhs  ) 

Assignment operator.

bool operator== ( const Feature rhs  )  const

Equality operator.

const std::vector<PeptideIdentification>& getPeptideIdentifications (  )  const [inline]

returns a const reference to the PeptideIdentification vector

std::vector<PeptideIdentification>& getPeptideIdentifications (  )  [inline]

returns a mutable reference to the PeptideIdentification vector

void setPeptideIdentifications ( const std::vector< PeptideIdentification > &  identifications  )  [inline]

sets the PeptideIdentification vector


Member Data Documentation

QualityType overall_quality_ [protected]

Overall quality measure of the feature.

QualityType qualities_[2] [protected]

Quality measures for each dimension.

ModelDescription<2> model_desc_ [protected]

Description of the theoretical model the feature was constructed with.

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).

ConvexHull2D convex_hull_ [mutable, protected]

Overall convex hull of the feature.

ChargeType charge_ [protected]

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

std::vector<PeptideIdentification> identifications_ [protected]

Peptide PeptideIdentifications belonging to the feature.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:45 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1