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

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	getDeleteCosts() Returns the costs for a delete gap, i.e., a gap in the second string.
double	getInsertCosts() Returns the costs for an insert gap, i.e., a gap in the first string.

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)

getInsertCosts

double getInsertCosts()

Returns the costs for an insert gap, i.e., a gap in the first string.

Returns:

the costs for an insert gap

getDeleteCosts

double getDeleteCosts()

Returns the costs for a delete gap, i.e., a gap in the second string.

Returns:

the costs for a delete gap