Package org.snpeff.binseq

Class DnaSequenceByte

java.lang.Object

org.snpeff.binseq.DnaSequenceByte

public class DnaSequenceByte
extends java.lang.Object

Binary packed DNA sequence.

Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'bytes; - Most significant bits are the first bases in the sequence (makes comparison easier)

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static byte[]	BASE2CODE
static char[]	BASES
static int	BASES_PER_BYTE
static int	BITS_PER_BASE
static byte[]	MASK

Constructor Summary

Constructors

Constructor	Description
DnaSequenceByte(int length, byte[] codes)
DnaSequenceByte(java.lang.String seqStr)

Method Summary

Modifier and Type	Method	Description
char	getBase(int index)
byte[]	getCodes()
int	getLength()
int	hashCode()
int	length()	Sequence lenth
void	set(java.lang.String seqStr)	Set sequence
java.lang.String	toString()
java.lang.String	toStringHex()

Methods inherited from class java.lang.Object

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

Field Detail

BASES_PER_BYTE

public static final int BASES_PER_BYTE

See Also:

Constant Field Values

BITS_PER_BASE

public static final int BITS_PER_BASE

See Also:

Constant Field Values

MASK

public static final byte[] MASK

BASES

public static final char[] BASES

BASE2CODE

public static final byte[] BASE2CODE

Constructor Detail

DnaSequenceByte

public DnaSequenceByte(int length,
                       byte[] codes)

DnaSequenceByte

public DnaSequenceByte(java.lang.String seqStr)

Method Detail

getBase

public char getBase(int index)

getCodes

public byte[] getCodes()

getLength

public int getLength()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

length

public int length()

Sequence lenth

set

public void set(java.lang.String seqStr)

Set sequence

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toStringHex

public java.lang.String toStringHex()