See: Description
| Interface | Description |
|---|---|
| Costs |
The general interface for the costs of an alignment.
|
| Class | Description |
|---|---|
| AffineCosts |
This class implements affine gap costs, i.e., the costs for starting a new gap are given by
start, and
the costs for elongating a gap by one position are given by elong. |
| MatrixCosts |
Class for matrix costs, i.e., the cost of any match/mismatch is stored in
a matrix allowing a huge degree of freedom.
|
| SimpleCosts |
Class for simple costs with costs
match for a match,
mismatch for a mismatch, and
gap for a gap (of length 1).
|