org.utgenome.util.aligner
Class SmithWatermanAligner.StringWrapper

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

All Implemented Interfaces:

GenomeSequence

Enclosing class:

SmithWatermanAligner

public static class SmithWatermanAligner.StringWrapper
extends Object
implements GenomeSequence

Field Summary

String

seq

Constructor Summary

SmithWatermanAligner.StringWrapper(String seq)

Method Summary

char	charAt(int index)
int	length()

Methods inherited from class java.lang.Object

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

Field Detail

seq

public final String seq

Constructor Detail

SmithWatermanAligner.StringWrapper

public SmithWatermanAligner.StringWrapper(String seq)

Method Detail

charAt

public char charAt(int index)

Specified by:

charAt in interface GenomeSequence

Parameters:

index - index on the genome sequence (0-origin)

Returns:

length

public int length()

Specified by:

length in interface GenomeSequence