Package org.snpeff.binseq
Class DnaSequenceByte
- java.lang.Object
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- org.snpeff.binseq.DnaSequenceByte
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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
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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
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Constructor Summary
Constructors Constructor Description DnaSequenceByte(int length, byte[] codes)
DnaSequenceByte(java.lang.String seqStr)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description char
getBase(int index)
byte[]
getCodes()
int
getLength()
int
hashCode()
int
length()
Sequence lenthvoid
set(java.lang.String seqStr)
Set sequencejava.lang.String
toString()
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Field Detail
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BASES_PER_BYTE
public static final int BASES_PER_BYTE
- See Also:
- Constant Field Values
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BITS_PER_BASE
public static final int BITS_PER_BASE
- See Also:
- Constant Field Values
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MASK
public static final byte[] MASK
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BASES
public static final char[] BASES
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BASE2CODE
public static final byte[] BASE2CODE
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Method Detail
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getBase
public char getBase(int index)
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getCodes
public byte[] getCodes()
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getLength
public int getLength()
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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length
public int length()
Sequence lenth- Returns:
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set
public void set(java.lang.String seqStr)
Set sequence- Parameters:
seqStr
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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