A map feature grouping algorithm for unlabeled data. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmUnlabeled.h>
Inheritance diagram for FeatureGroupingAlgorithmUnlabeled:
Public Member Functions | |
| FeatureGroupingAlgorithmUnlabeled () | |
| Default constructor. | |
| virtual | ~FeatureGroupingAlgorithmUnlabeled () |
| Destructor. | |
| virtual void | group (const std::vector< FeatureMap<> > &maps, ConsensusMap &out) |
| Applies the algorithm. | |
Static Public Member Functions | |
| static FeatureGroupingAlgorithm * | create () |
| Creates a new instance of this class (for Factory). | |
| static String | getProductName () |
| Returns the product name (for the Factory). | |
Private Member Functions | |
| FeatureGroupingAlgorithmUnlabeled (const FeatureGroupingAlgorithmUnlabeled &) | |
| Copy constructor intentionally not implemented -> private. | |
| FeatureGroupingAlgorithmUnlabeled & | operator= (const FeatureGroupingAlgorithmUnlabeled &) |
| Assignment operator intentionally not implemented -> private. | |
Detailed Description
A map feature grouping algorithm for unlabeled data.
It takes many maps and searches for corresponding features. The corresponding features must be aligned, but may have small position deviations.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| second_nearest_gap | float | 2 | min: 1 | The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself. |
| use_identifications | string | false | true, false | Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account). |
| ignore_charge | string | false | true, false | Compare features normally even if their charge states are different |
| distance_RT:max_difference | float | 100 | min: 0 | Maximum allowed difference in RT in seconds |
| distance_RT:exponent | float | 1 | min: 0 | Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
| distance_RT:weight | float | 1 | min: 0 | RT distances are weighted by this factor |
| distance_MZ:max_difference | float | 0.3 | min: 0 | Maximum allowed difference in m/z (unit defined by 'unit') |
| distance_MZ:unit | string | Da | Da, ppm | Unit of the 'max_difference' parameter |
| distance_MZ:exponent | float | 2 | min: 0 | Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
| distance_MZ:weight | float | 1 | min: 0 | m/z distances are weighted by this factor |
| distance_intensity:exponent | float | 1 | min: 0 | Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
| distance_intensity:weight | float | 0 | min: 0 | Distances based on relative intensity are weighted by this factor |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
Default constructor.
| virtual ~FeatureGroupingAlgorithmUnlabeled | ( | ) | [virtual] |
Destructor.
| FeatureGroupingAlgorithmUnlabeled | ( | const FeatureGroupingAlgorithmUnlabeled & | ) | [private] |
Copy constructor intentionally not implemented -> private.
Member Function Documentation
| static FeatureGroupingAlgorithm* create | ( | ) | [inline, static] |
Creates a new instance of this class (for Factory).
| virtual void group | ( | const std::vector< FeatureMap<> > & | maps, | |
| ConsensusMap & | out | |||
| ) | [virtual] |
Applies the algorithm.
- Exceptions:
-
IllegalArgument is thrown if less than two input maps are given.
Implements FeatureGroupingAlgorithm.
| FeatureGroupingAlgorithmUnlabeled& operator= | ( | const FeatureGroupingAlgorithmUnlabeled & | ) | [private] |
Assignment operator intentionally not implemented -> private.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |