#include <OpenMS/KERNEL/Feature.h>
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 ChargeType & | getCharge () const |
Non-mutable access to charge state. | |
void | setCharge (const ChargeType &ch) |
Set charge state. | |
Feature & | operator= (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. | |
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 | 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< 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. | |
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... |
typedef DoubleReal QualityType |
Type of the quality values.
typedef Int ChargeType |
Charge type.
Feature | ( | ) | [inline] |
Default constructor.
~Feature | ( | ) | [inline] |
Destructor.
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).
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
.
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
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.
Generated Tue Apr 1 15:36:45 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |