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.