org.utgenome.util.aligner
Class SuffixArrayBuilder

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

public class SuffixArrayBuilder
extends Object

SA-IS implementation for building suffix arrays

Author:

leo

Nested Class Summary

static class	SuffixArrayBuilder.StringWrapper
static class	SuffixArrayBuilder.SubArray

Constructor Summary

SuffixArrayBuilder(RandomAccess input, int N, int K)

SuffixArrayBuilder(String input)

Method Summary

int[]	SAIS()
void	SAIS(int[] SA)

Methods inherited from class java.lang.Object

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

Constructor Detail

SuffixArrayBuilder

public SuffixArrayBuilder(RandomAccess input,
                          int N,
                          int K)

SuffixArrayBuilder

public SuffixArrayBuilder(String input)

Method Detail

SAIS

public int[] SAIS()

SAIS

public void SAIS(int[] SA)