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java.lang.Objectde.jstacs.algorithms.Alignment
public class Alignment
Class for gapped global alignments using the extended Needleman-Wunsch algorithm.
Nested Class Summary | |
---|---|
static interface |
Alignment.Costs
The general interface for the costs of an alignment. |
static class |
Alignment.SimpleCosts
Class for simple costs with costs mismatch for a mismatch,
costs start to start a new gap, costs elong to
elongate a gap by one position and costs of 0 for a match. |
static class |
Alignment.StringAlignment
Class for the representation of an alignment of two String s. |
Constructor Summary | |
---|---|
Alignment(Sequence s1,
Sequence s2,
Alignment.Costs costs)
Creates a new Alignment.StringAlignment instance that aligns the sequences
s1 and s2 using the costs defined in
costs . |
Method Summary | |
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Alignment.StringAlignment |
getAlignment()
Computes and returns the alignment of s1 and s2
(Alignment(Sequence, Sequence, Costs) ). |
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 Alignment(Sequence s1, Sequence s2, Alignment.Costs costs)
Alignment.StringAlignment
instance that aligns the sequences
s1
and s2
using the costs defined in
costs
.
s1
- the first sequences2
- the second sequencecosts
- the costsMethod Detail |
---|
public Alignment.StringAlignment getAlignment()
s1
and s2
(Alignment(Sequence, Sequence, Costs)
).
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