Package htsjdk.samtools.cram.structure

Enum Class EncodingID

java.lang.Object

java.lang.Enum<EncodingID>

htsjdk.samtools.cram.structure.EncodingID

All Implemented Interfaces:

Serializable, Comparable<EncodingID>, Constable

public enum EncodingID
extends Enum<EncodingID>

Encoding ID as specified by Section 3 of the CRAM spec. These are basically ways to serialize a data series.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
BETA	Binary coding with sufficient leading 0 bits to store each value with the same length
BYTE_ARRAY_LEN	A byte array serialized as [length][elements]
BYTE_ARRAY_STOP	A byte array serialized as [elements][stop]
EXTERNAL	Shove the data into a byte array for compressing later with a generic compressor like GZIP.
GAMMA	http://en.wikipedia.org/wiki/Elias_gamma_coding
GOLOMB	EXPERIMENTAL: This encoding is untested and scheduled for removal from the CRAM spec.
GOLOMB_RICE	EXPERIMENTAL: This encoding is untested and scheduled for removal from the CRAM spec.
HUFFMAN	http://en.wikipedia.org/wiki/Huffman_coding
NULL	"Do nothing" encoding.
SUBEXPONENTIAL	Subexponential codes.

Method Summary

Modifier and Type	Method	Description
int	getId()
boolean	isExternalEncoding()	Return true if this encoding can be used in an external block.
static EncodingID	valueOf(String name)	Returns the enum constant of this class with the specified name.
static EncodingID[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

NULL

public static final EncodingID NULL

"Do nothing" encoding. Should throw an exception when trying reading or writing with this encoding.

EXTERNAL

public static final EncodingID EXTERNAL

Shove the data into a byte array for compressing later with a generic compressor like GZIP.

GOLOMB

public static final EncodingID GOLOMB

EXPERIMENTAL: This encoding is untested and scheduled for removal from the CRAM spec. http://en.wikipedia.org/wiki/Golomb_coding

HUFFMAN

public static final EncodingID HUFFMAN

http://en.wikipedia.org/wiki/Huffman_coding

BYTE_ARRAY_LEN

public static final EncodingID BYTE_ARRAY_LEN

A byte array serialized as [length][elements]

BYTE_ARRAY_STOP

public static final EncodingID BYTE_ARRAY_STOP

A byte array serialized as [elements][stop]

BETA

public static final EncodingID BETA

Binary coding with sufficient leading 0 bits to store each value with the same length

SUBEXPONENTIAL

public static final EncodingID SUBEXPONENTIAL

Subexponential codes. http://www.ittc.ku.edu/~jsv/Papers/HoV94.progressive_FELICS.pdf

GOLOMB_RICE

public static final EncodingID GOLOMB_RICE

EXPERIMENTAL: This encoding is untested and scheduled for removal from the CRAM spec. A variant of GOLOMB encoding: http://en.wikipedia.org/wiki/Golomb_coding

GAMMA

public static final EncodingID GAMMA

http://en.wikipedia.org/wiki/Elias_gamma_coding

Method Details

values

public static EncodingID[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static EncodingID valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null

getId

public int getId()

Returns:

the number assigned to each encoding in the CRAM spec

isExternalEncoding

public boolean isExternalEncoding()

Return true if this encoding can be used in an external block. This returns true even for BYTE_ARRAY_LEN, even though BYTE_ARRAY_LEN is not entirely restricted to external, since it can use a core encoding for the array length sub-encoding.

Returns:

true if the encoding is EXTERNAL, BYTE_ARRAY_STOP, or BYTE_ARRAY_LEN.