htsjdk.samtools.cram.structure

Enum EncodingID

java.lang.Object

java.lang.Enum<EncodingID>

htsjdk.samtools.cram.structure.EncodingID

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<EncodingID>

public enum EncodingID
extends java.lang.Enum<EncodingID>

Encoding ID as defined in the CRAM specs. These are basically ways to serialize a data series.

Enum Constant Summary

Enum Constants

Enum Constant and Description
BETA http://en.wikipedia.org/wiki/Beta_Code
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 'naf said: http://en.wikipedia.org/wiki/Golomb_coding
GOLOMB_RICE A variant of GOLOMB encoding: http://en.wikipedia.org/wiki/Golomb_coding
HUFFMAN http://en.wikipedia.org/wiki/Huffman_coding
NULL "Do nothing" encoding.
SUBEXPONENTIAL Subexponential codes, see the CRAM specs for details.

Method Summary

Modifier and Type	Method and Description
static EncodingID	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static EncodingID[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

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

'naf said: 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

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

SUBEXPONENTIAL

public static final EncodingID SUBEXPONENTIAL

Subexponential codes, see the CRAM specs for details.

GOLOMB_RICE

public static final EncodingID GOLOMB_RICE

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 Detail

values

public static EncodingID[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (EncodingID c : EncodingID.values())
    System.out.println(c);

Returns:

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

valueOf

public static EncodingID valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null