org.utgenome.util.aligner
Class SmithWatermanAligner

java.lang.Object
  org.utgenome.util.aligner.SmithWatermanAligner

public class SmithWatermanAligner
extends Object

Simple Smith-Waterman based aligner

Author:

leo

Nested Class Summary

static class	SmithWatermanAligner.Alignment
static class	SmithWatermanAligner.Config
static class	SmithWatermanAligner.StringWrapper

Constructor Summary

SmithWatermanAligner()

SmithWatermanAligner(SmithWatermanAligner.Config config)

Method Summary

<Seq1 extends GenomeSequence,Seq2 extends GenomeSequence> SmithWatermanAligner.Alignment	align(Seq1 seq1, Seq2 seq2)
SmithWatermanAligner.Alignment	align(String seq1, String seq2)
static GenomeSequence	wrap(String seq) Wrap the input string as GenomeSequence

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SmithWatermanAligner

public SmithWatermanAligner()

SmithWatermanAligner

public SmithWatermanAligner(SmithWatermanAligner.Config config)

Method Detail

wrap

public static GenomeSequence wrap(String seq)

Wrap the input string as GenomeSequence

Parameters:

seq -

Returns:

align

public SmithWatermanAligner.Alignment align(String seq1,
                                            String seq2)

align

public <Seq1 extends GenomeSequence,Seq2 extends GenomeSequence> SmithWatermanAligner.Alignment align(Seq1 seq1,
                                                                                                      Seq2 seq2)