htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteCodec Maven / Gradle / Ivy
/**
* ****************************************************************************
* 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.encoding.core;
import htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanByteHelper;
import htsjdk.samtools.cram.io.BitInputStream;
import htsjdk.samtools.cram.io.BitOutputStream;
/**
* Encode Bytes using the Canonical Huffman Codec.
* https://en.wikipedia.org/wiki/Canonical_Huffman_code
*/
class CanonicalHuffmanByteCodec extends CoreCodec {
private final HuffmanByteHelper helper;
/**
* Construct a Canonical Huffman Codec for Byte data
*
* @param coreBlockInputStream the input bitstream to read from
* @param coreBlockOutputStream the output bitstream to write to
* @param values the alphabet (provided as Integers)
* @param bitLengths the number of bits of symbol's huffman code
*/
public CanonicalHuffmanByteCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream,
final byte[] values, final int[] bitLengths) {
super(coreBlockInputStream, coreBlockOutputStream);
helper = new HuffmanByteHelper(values, bitLengths);
}
@Override
public Byte read() {
return helper.read(coreBlockInputStream);
}
@Override
public void write(final Byte value) {
helper.write(coreBlockOutputStream, value);
}
@Override
public Byte read(final int length) {
throw new RuntimeException("Not implemented");
}
}