de.jstacs.algorithms.alignment.cost

Interface Costs

All Superinterfaces:

Storable

All Known Implementing Classes:

AffineCosts, MatrixCosts, SimpleCosts

public interface Costs
extends Storable

The general interface for the costs of an alignment.

Author:

Jan Grau

Method Summary

Methods

Modifier and Type	Method and Description
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.

Methods inherited from interface de.jstacs.Storable

toXML

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