de.jstacs.algorithms.alignment.cost
Interface Costs

All Known Implementing Classes:

AffineCosts, MatrixCosts, SimpleCosts

public interface Costs

The general interface for the costs of an alignment.

Author:

Jan Grau

Method Summary

double	getCostFor(Sequence s1, Sequence s2, int i, int j) Returns the costs for the alignment of s1(i) and s2(j).
double	getGapCosts() Returns the costs for a gap.

Method Detail

getCostFor

double getCostFor(Sequence s1,
                  Sequence s2,
                  int i,
                  int j)

Returns the costs for the alignment of s1(i) and s2(j).

Parameters:

s1 - the first sequence

s2 - the second sequence

i - the index in the first sequence

j - the index in the second sequence

Returns:

the costs

See Also:

Sequence.discreteVal(int)

getGapCosts

double getGapCosts()

Returns the costs for a gap.

Returns:

the costs for a gap