org.utgenome.gwt.utgb.client.bio
Class ACGTEncoder

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.ACGTEncoder

public class ACGTEncoder
extends Object

Nucleotide ACGT <-> 2bit code conversion utility

Author:

leo

Constructor Summary

ACGTEncoder()

Method Summary

static byte	to2bitCode(char base)
static char	toBase(int code)
static int	toKmerInt(int K, String acgt) Return the k-mer interger of the given ACGT sequence
static String	toString(int kmerInt, int K)

Methods inherited from class java.lang.Object

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

Constructor Detail

ACGTEncoder

public ACGTEncoder()

Method Detail

to2bitCode

public static byte to2bitCode(char base)

toBase

public static char toBase(int code)

toKmerInt

public static int toKmerInt(int K,
                            String acgt)

Return the k-mer interger of the given ACGT sequence

Parameters:

K -

acgt -

Returns:

k-mer integer of the sequence, or -1 when N or the other invalid characters are contained in the sequence

toString

public static String toString(int kmerInt,
                              int K)