See: Description
Interface | Description |
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Costs |
The general interface for the costs of an alignment.
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Class | Description |
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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.
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SimpleCosts |
Class for simple costs with costs
match for a match,
mismatch for a mismatch, and
gap for a gap (of length 1).
|