/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.compress.huffman;

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;

/**
 * Compression application using adaptive Huffman coding.
 * <p>Usage: java AdaptiveHuffmanCompress InputFile OutputFile</p>
 * <p>Then use the corresponding "AdaptiveHuffmanDecompress" application to recreate the original input file.</p>
 * <p>Note that the application starts with a flat frequency table of 257 symbols (all set to a frequency of 1),
 * collects statistics while bytes are being encoded, and regenerates the Huffman code periodically. The
 * corresponding decompressor program also starts with a flat frequency table, updates it while bytes are being
 * decoded, and regenerates the Huffman code periodically at the exact same points in time. It is by design that
 * the compressor and decompressor have synchronized states, so that the data can be decompressed properly.</p>
 */
public final class AdaptiveHuffmanCompress {

    // Command line main application function.
    public static void main(String[] args) throws IOException {
        // Handle command line arguments
        if (args.length != 2) {
            System.err.println("Usage: java AdaptiveHuffmanCompress InputFile OutputFile");
            System.exit(1);
            return;
        }
        File inputFile = new File(args[0]);
        File outputFile = new File(args[1]);

        // Perform file compression
        InputStream in = new BufferedInputStream(new FileInputStream(inputFile));
        BitOutputStream out = new BitOutputStream(new BufferedOutputStream(new FileOutputStream(outputFile)));
        try {
            compress(in, out);
        } finally {
            out.close();
            in.close();
        }
    }


    // To allow unit testing, this method is package-private instead of private.
    public static void compress(InputStream in, BitOutputStream out) throws IOException {
        int[] initFreqs = new int[257];
        Arrays.fill(initFreqs, 1);

        FrequencyTable freqs = new FrequencyTable(initFreqs);
        HuffmanEncoder enc = new HuffmanEncoder(out);
        enc.codeTree = freqs.buildCodeTree();  // Don't need to make canonical code because we don't transmit the code tree
        int count = 0;  // Number of bytes read from the input file
        while (true) {
            // Read and encode one byte
            int symbol = in.read();
            if (symbol == -1)
                break;
            enc.write(symbol);
            count++;

            // Update the frequency table and possibly the code tree
            freqs.increment(symbol);
            if (count < 262144 && isPowerOf2(count) || count % 262144 == 0)  // Update code tree
                enc.codeTree = freqs.buildCodeTree();
            if (count % 262144 == 0)  // Reset frequency table
                freqs = new FrequencyTable(initFreqs);
        }
        enc.write(256);  // EOF
    }


    private static boolean isPowerOf2(int x) {
        return x > 0 && Integer.bitCount(x) == 1;
    }

}