A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.h>
Public Member Functions | |
| PoseClusteringAffineSuperimposer () | |
| Default ctor. | |
| virtual | ~PoseClusteringAffineSuperimposer () |
| Destructor. | |
| virtual void | run (const ConsensusMap &map_model, const ConsensusMap &map_scene, TransformationDescription &transformation) |
| Estimates the transformation and fills the given mapping function. (Has a precondition!). | |
Static Public Member Functions | |
| static BaseSuperimposer * | create () |
| Returns an instance of this class. | |
| static const String | getProductName () |
| Returns the name of this module. | |
Detailed Description
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation.
This algorithm works on two consensus maps. It computes an affine transformation that maps the elements of second map as near as possible to the elements in the first map.
The voting scheme hashes affine transformations between pairs of features in map one and pairs of features in map two. Each such pair of pairs defines a (potential) "pose" of the second map relative to the first. Then it finds a cluster in the parameter space of these poses. The affine transformation is then computed from this cluster of potential poses, hence the name pose clustering.
- See also:
- PoseClusteringShiftSuperimposer
| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| mz_pair_max_distance | float | 0.5 | min: 0 | Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing. |
| rt_pair_distance_fraction | float | 0.1 | min: 0 max: 1 | Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). |
| num_used_points | int | 2000 | min: -1 | Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1. |
| scaling_bucket_size | float | 0.005 | min: 0 | The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs. |
| shift_bucket_size | float | 3 | min: 0 | The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans. |
| max_shift | float | 1000 | min: 0 | Maximal shift which is considered during histogramming. This applies for both directions. |
| max_scaling | float | 2 | min: 1 | Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this. |
| dump_buckets | string | [DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically. | ||
| dump_pairs | string | [DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
Default ctor.
| virtual ~PoseClusteringAffineSuperimposer | ( | ) | [inline, virtual] |
Destructor.
Member Function Documentation
| static BaseSuperimposer* create | ( | ) | [inline, static] |
Returns an instance of this class.
| static const String getProductName | ( | ) | [inline, static] |
Returns the name of this module.
| virtual void run | ( | const ConsensusMap & | map_model, | |
| const ConsensusMap & | map_scene, | |||
| TransformationDescription & | transformation | |||
| ) | [virtual] |
Estimates the transformation and fills the given mapping function. (Has a precondition!).
- Note:
- Exactly two input maps must be given.
- Precondition:
- For performance reasons, we trust that (the equivalent of:)
maps[0].updateRanges(); maps[1].updateRanges();
has been done before calling this. You have been warned!
- Exceptions:
-
IllegalArgument is thrown if the input maps are invalid.
Implements BaseSuperimposer.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |