org.utgenome.util.aligner
Class SmithWatermanAligner

java.lang.Object
  extended by 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)


Copyright © 2007-2011 utgenome.org. All Rights Reserved.