Uses of Package
de.jstacs.algorithms.alignment.cost

Packages that use de.jstacs.algorithms.alignment.cost

de.jstacs.algorithms.alignment	Provides classes for alignments
de.jstacs.algorithms.alignment.cost	Provides classes for cost functions used in alignments

Classes in de.jstacs.algorithms.alignment.cost used by de.jstacs.algorithms.alignment

Costs
The general interface for the costs of an alignment.

Classes in de.jstacs.algorithms.alignment.cost used by de.jstacs.algorithms.alignment.cost

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.

Costs
The general interface for the costs of an alignment.

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