Enum EncodingID

    • 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
        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 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​(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:
        IllegalArgumentException - if this enum type 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.