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See:
Description
Interface Summary | |
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Costs | The general interface for the costs of an alignment. |
Class Summary | |
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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. |
SimpleCosts | Class for simple costs with costs
match for a match,
mismatch for a mismatch, and
gap for a gap (of length 1). |
Provides classes for cost functions used in alignments.
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