| ClusterBuilder Class |
Clustering is a process in which individual matches are grouped in larger
set called Cluster. The matches in cluster are decided based on paramters
like fixed difference allowed, maximum difference allowed, minimum score
and separation factor that should be satisfied.
This class implements IClusterBuilder interface.
Inheritance HierarchyNamespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe ClusterBuilder type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | ClusterBuilder |
Initializes a new instance of the ClusterBuilder class
|
Properties| Name | Description | |
|---|---|---|
 | FixedSeparation |
Gets or sets maximum fixed diagonal difference
|
| MaximumSeparation |
Gets or sets maximum separation between the adjacent matches in clusters
|
| MinimumScore |
Gets or sets minimum output score
|
| ScoreMethod |
Gets or sets the method to use while calculating score of a cluster.
Default is MatchLength.
|
| SeparationFactor |
Gets or sets separation factor. Fraction equal to
(diagonal difference / match separation) where higher values
increase the insertion or deletion (indel) tolerance
|
Methods| Name | Description | |
|---|---|---|
| BuildClusters(ListMatchExtension) |
Get the Cluster from given inputs of matches.
Steps are as follows:
1. Sort MUMs based on query sequence start.
2. Removing overlapping MUMs (in both sequences) and MUMs with same
diagonal offset (usually adjacent)
3. Check for separation between two MUMs
4. Check the diagonal separation
5. If MUMs passes above conditions merge them in one cluster.
6. Sort MUMs using cluster id
7. Process clusters (Joining clusters) |
| BuildClusters(ListMatchExtension, Boolean) |
Get the Cluster from given inputs of matches.
Steps are as follows:
1. Sort MUMs based on query sequence start (if sortedByQuerySequenceIndex is false)
2. Removing overlapping MUMs (in both sequences) and MUMs with same
diagonal offset (usually adjacent)
3. Check for separation between two MUMs
4. Check the diagonal separation
5. If MUMs passes above conditions merge them in one cluster.
6. Sort MUMs using cluster id
7. Process clusters (Joining clusters) |
| Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) |
 | Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) |
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
See Also