See: Description
Interface  Description 

Costs 
The general interface for the costs of an alignment.

Class  Description 

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).
