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public interface Costs
The general interface for the costs of an alignment.
Method Summary | |
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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 |
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double getCostFor(Sequence s1, Sequence s2, int i, int j)
s1(i)
and
s2(j)
.
s1
- the first sequences2
- the second sequencei
- the index in the first sequencej
- the index in the second sequence
Sequence.discreteVal(int)
double getGapCosts()
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