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## Uses of Interface
de.jstacs.algorithms.alignment.cost.Costs

Packages that use Costs
de.jstacs.algorithms.alignment | Provides classes for alignments
de.jstacs.algorithms.alignment.cost | Provides classes for cost functions used in alignments

Uses of Costs in de.jstacs.algorithms.alignment

Constructors in de.jstacs.algorithms.alignment with parameters of type Costs
`Alignment(Alignment.AlignmentType type, Costs costs)` Creates a new `Alignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs`.
`Alignment(Alignment.AlignmentType type, Costs costs, int offDiagonal)` Creates a new `Alignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs` and a banded version of the alignment algorithm.

Uses of Costs in de.jstacs.algorithms.alignment.cost

Classes in de.jstacs.algorithms.alignment.cost that implement Costs
`class` | `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`.
`class` | `MatrixCosts` Class for matrix costs, i.e., the cost of any match/mismatch is stored in a matrix allowing a huge degree of freedom.
`class` | `SimpleCosts` Class for simple costs with costs `match` for a match, `mismatch` for a mismatch, and `gap` for a gap (of length 1).

Constructors in de.jstacs.algorithms.alignment.cost with parameters of type Costs
`AffineCosts(double start, Costs c)` This constructor creates a new instance of cost using affine gap costs.

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