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