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java.lang.Objectde.jstacs.algorithms.alignment.cost.SimpleCosts
public class SimpleCosts
Class for simple costs with costs
match
for a match,mismatch
for a mismatch, andgap
for a gap (of length 1).
Constructor Summary | |
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SimpleCosts(double match,
double mismatch,
double gap)
Creates a new instance of simple costs with costs match for a match,
mismatch for a mismatch, and
gap for a gap (of length 1). |
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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SimpleCosts(double match, double mismatch, double gap)
match
for a match,
mismatch
for a mismatch, and
gap
for a gap (of length 1).
match
- the match costsmismatch
- the mismatch costsgap
- the costs for a gapMethod Detail |
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public double getCostFor(Sequence s1, Sequence s2, int i, int j)
Costs
s1(i)
and
s2(j)
.
getCostFor
in interface Costs
s1
- the first sequences2
- the second sequencei
- the index in the first sequencej
- the index in the second sequence
Sequence.discreteVal(int)
public double getGapCosts()
Costs
getGapCosts
in interface Costs
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