htsjdk.samtools.cram.structure.EncodingID Maven / Gradle / Ivy

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A Java API for high-throughput sequencing data (HTS) formats
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/**
 * ****************************************************************************
 * Copyright 2013 EMBL-EBI
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 

 * http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 * ****************************************************************************
 */
package htsjdk.samtools.cram.structure;

/**
 * Encoding ID as specified by Section 3 of the CRAM spec. These are basically ways to serialize a data series.
 */
public enum EncodingID {
    /**
     * "Do nothing" encoding. Should throw an exception when trying reading or writing with this encoding.
     */
    NULL(0),

    /**
     * Shove the data into a byte array for compressing later with a generic compressor like GZIP.
     */
    EXTERNAL(1),

    /**
     * EXPERIMENTAL: This encoding is untested and scheduled for removal from the CRAM spec.
     * http://en.wikipedia.org/wiki/Golomb_coding
     */
    GOLOMB(2),

    /**
     * http://en.wikipedia.org/wiki/Huffman_coding
     */
    HUFFMAN(3),

    /**
     * A byte array serialized as [length][elements]
     */
    BYTE_ARRAY_LEN(4),

    /**
     * A byte array serialized as [elements][stop]
     */
    BYTE_ARRAY_STOP(5),

    /**
     * Binary coding with sufficient leading 0 bits to store each value with the same length
     */
    BETA(6),

    /**
     * Subexponential codes.
     * http://www.ittc.ku.edu/~jsv/Papers/HoV94.progressive_FELICS.pdf
     */
    SUBEXPONENTIAL(7),

    /**
     * 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
     */
    GOLOMB_RICE(8),

    /**
     * http://en.wikipedia.org/wiki/Elias_gamma_coding
     */
    GAMMA(9);

    private final int id;

    /**
     * The encodings specified by Section 3 of the CRAM spec
     * @param id the number assigned to each encoding in the CRAM spec
     */
    EncodingID(final int id) {
        this.id = id;
    }

    /**
     * @return the number assigned to each encoding in the CRAM spec
     */
    public int getId() {
        return id;
    }

    /**
     * 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.
     * @return true if the encoding is EXTERNAL, BYTE_ARRAY_STOP, or BYTE_ARRAY_LEN.
     */
    public boolean isExternalEncoding() {
        return this == EXTERNAL || this == BYTE_ARRAY_LEN || this == BYTE_ARRAY_STOP;
    }
}