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## 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

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