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## Package de.jstacs.algorithms.alignment.cost

Provides classes for cost functions used in alignments

See:
Description

Interface Summary
Costs | The general interface for the costs of an alignment.

Class Summary
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 `mismatch` for a mismatch, costs `start` to start a new gap, costs `elong` to elongate a gap by one position and costs of `match` for a match.

Enum Summary
Costs.Direction | The direction of the predecessor in the DP (dynamic programming)-matrix.

## Package de.jstacs.algorithms.alignment.cost Description

Provides classes for cost functions used in alignments.

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