A basic LC-MS feature. More...
#include <OpenMS/KERNEL/BaseFeature.h>
Classes | |
| struct | QualityLess |
| Compare by quality. More... | |
Public Types | |
Type definitions | |
| typedef Real | QualityType |
| Type of quality values. | |
| typedef Int | ChargeType |
| Type of charge values. | |
| typedef Real | WidthType |
| Type of feature width/FWHM (RT). | |
Public Member Functions | |
| 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) |
| Assignment operator. | |
| bool | operator== (const BaseFeature &rhs) const |
| Equality operator. | |
| bool | operator!= (const BaseFeature &rhs) const |
| Unequality 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 > &peptides) |
| sets the PeptideIdentification vector | |
Constructors and Destructor | |
| BaseFeature () | |
| Default constructor. | |
| BaseFeature (const BaseFeature &feature) | |
| Copy constructor. | |
| BaseFeature (const Peak2D &point) | |
| Constructor from raw data point. | |
| BaseFeature (const RichPeak2D &point) | |
| Constructor from raw data point with meta information. | |
| ~BaseFeature () | |
| Destructor. | |
Quality methods | |
| QualityType | getQuality () const |
| Non-mutable access to the overall quality. | |
| void | setQuality (QualityType q) |
| Set the overall quality. | |
Protected Attributes | |
| 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. | |
| std::vector < PeptideIdentification > | peptides_ |
| Peptide PeptideIdentifications belonging to the feature. | |
Detailed Description
A basic LC-MS feature.
This class represents a "minimal" feature, defined by a position in RT and m/z, intensity, charge, quality, and annotated peptides. Most classes dealing with features will use the subclasses Feature or ConsensusFeature directly. However, algorithms that rely on very general characteristics of features can use this class to provide a unified solution for both "normal" features and consensus features.
Member Typedef Documentation
| typedef Int ChargeType |
Type of charge values.
| typedef Real QualityType |
Type of quality values.
Constructor & Destructor Documentation
| BaseFeature | ( | ) |
Default constructor.
| BaseFeature | ( | const BaseFeature & | feature | ) |
Copy constructor.
| BaseFeature | ( | const Peak2D & | point | ) | [explicit] |
Constructor from raw data point.
| BaseFeature | ( | const RichPeak2D & | point | ) | [explicit] |
Constructor from raw data point with meta information.
| ~BaseFeature | ( | ) |
Destructor.
Member Function Documentation
| const ChargeType& getCharge | ( | ) | const |
Non-mutable access to charge state.
Referenced by IDMapper::annotate(), ModelFitter< PeakType, FeatureType >::fit(), KroenikFile::load(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
| const std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) | const |
returns a const reference to the PeptideIdentification vector
Referenced by IDMapper::annotate().
| std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) |
returns a mutable reference to the PeptideIdentification vector
| QualityType getQuality | ( | ) | const |
Non-mutable access to the overall quality.
Referenced by BaseFeature::QualityLess::operator()().
| WidthType getWidth | ( | ) | const |
Non-mutable access to the features width (full width at half max, FWHM).
| bool operator!= | ( | const BaseFeature & | rhs | ) | const |
Unequality operator.
| BaseFeature& operator= | ( | const BaseFeature & | rhs | ) |
Assignment operator.
| bool operator== | ( | const BaseFeature & | rhs | ) | const |
Equality operator.
| void setCharge | ( | const ChargeType & | ch | ) |
| void setPeptideIdentifications | ( | const std::vector< PeptideIdentification > & | peptides | ) |
sets the PeptideIdentification vector
| void setQuality | ( | QualityType | q | ) |
Set the overall quality.
| void setWidth | ( | WidthType | fwhm | ) |
Set the width of the feature (FWHM).
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
Member Data Documentation
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> peptides_ [protected] |
Peptide PeptideIdentifications belonging to the feature.
QualityType quality_ [protected] |
Overall quality measure of the feature.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1 |