/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
/*
 * @(#)UncompressInputStream.java           0.3-3 06/05/2001
 *
 *  This file is part of the HTTPClient package
 *  Copyright (C) 1996-2001 Ronald Tschalar
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2 of the License, or (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public
 *  License along with this library; if not, write to the Free
 *  Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
 *  MA 02111-1307, USA
 *
 *  For questions, suggestions, bug-reports, enhancement-requests etc.
 *  I may be contacted at:
 *
 *  ronald@xxxxxxxxxxxxx
 *
 *  The HTTPClient's home page is located at:
 *
 *  http://www.innovation.ch/java/HTTPClient/
 */

package org.biojava.nbio.core.util;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;


/**
 * This class decompresses an input stream containing data compressed with
 * the unix "compress" utility (LZC, a LZW variant). This code is based
 * heavily on the <var>unlzw.c</var> code in <var>gzip-1.2.4</var> (written
 * by Peter Jannesen) and the original compress code.
 *
 *
 *  This version has been modified from the original 0.3-3 version by the
 *  Unidata Program Center (support@xxxxxxxxxxxxxxxx) to make the constructor
 *  public and to fix a couple of bugs.
 *  Also:
 *   - markSupported() returns false
 *   - add uncompress() static method
 *
 * @version 0.3-3 06/05/2001
 * @author  Ronald Tschalar
 * @author  Unidata Program Center
 * @author  Richard Holland - making LZW_MAGIC package-visible.
 *
 * @version 0.3-5 2008/01/19
 * @author  Fred Hansen (zweibieren@yahoo.com)
 *      Fixed available() and the EOF condition for mainloop.
 *      Also added some comments.
 * 
 * @version 1.0 2018/01/08
 * @author      Fred Hansen (zweibieren@yahoo.com)
 *      added uncompress(InputStream,OutputStream)
 *          and called it from main(String[])
 *          and uncompress(String, FileOutputStream)
 *      normalize indentation 
 *      rewrite skip method
 *      amend logging code in uncompress(String, FileOutputStream)  
 */
public class UncompressInputStream extends FilterInputStream {
        private final static Logger logger 
                = LoggerFactory.getLogger(UncompressInputStream.class);

        /**
         * @param is the input stream to decompress
         * @throws IOException if the header is malformed
         */
        public UncompressInputStream(InputStream is) throws IOException {
                super(is);
                parse_header();
        }


        @Override
        public synchronized int read() throws IOException {
                byte[] one = new byte[1];
                int b = read(one, 0, 1);
                if (b == 1)
                        return (one[0] & 0xff);
                else
                        return -1;
        }


        // string table stuff
        private static final int TBL_CLEAR = 0x100;
        private static final int TBL_FIRST = TBL_CLEAR + 1;

        private int[] tab_prefix;
        private byte[] tab_suffix;
        final private int[] zeros = new int[256];
        private byte[] stack;

        // various state
        private boolean block_mode;
        private int n_bits;
        private int maxbits;
        private int maxmaxcode;
        private int maxcode;
        private int bitmask;
        private int oldcode;
        private byte finchar;
        private int stackp;
        private int free_ent;

        /* input buffer
                The input stream must be considered in chunks 
                Each chunk is of length eight times the current code length.
                Thus the chunk contains eight codes; NOT on byte boundaries.
        */
        final private byte[] data = new byte[10000];
        private int 
            bit_pos = 0,  // current bitwise location in bitstream
            end = 0,      // index of next byte to fill in data
            got = 0;      // number of bytes gotten by most recent read()
        private boolean eof = false;
        private static final int EXTRA = 64;


        @Override
        public synchronized int read(byte[] buf, int off, int len)
                        throws IOException {
                if (eof) return -1;
                int start = off;

                /* Using local copies of various variables speeds things up by as
                 * much as 30% !
                 */
                int[] l_tab_prefix = tab_prefix;
                byte[] l_tab_suffix = tab_suffix;
                byte[] l_stack = stack;
                int l_n_bits = n_bits;
                int l_maxcode = maxcode;
                int l_maxmaxcode = maxmaxcode;
                int l_bitmask = bitmask;
                int l_oldcode = oldcode;
                byte l_finchar = finchar;
                int l_stackp = stackp;
                int l_free_ent = free_ent;
                byte[] l_data = data;
                int l_bit_pos = bit_pos;

                // empty stack if stuff still left
                int s_size = l_stack.length - l_stackp;
                if (s_size > 0) {
                        int num = (s_size >= len) ? len : s_size;
                        System.arraycopy(l_stack, l_stackp, buf, off, num);
                        off += num;
                        len -= num;
                        l_stackp += num;
                }

                if (len == 0) {
                        stackp = l_stackp;
                        return off - start;
                }

                // loop, filling local buffer until enough data has been decompressed
                main_loop: do {
                        if (end < EXTRA) fill();

                        int bit_end = (got > 0) 
                            ?  (end - end % l_n_bits) << 3      // set to a "chunk" boundary
                            :  (end << 3) - (l_n_bits - 1);     // no more data, set to last code

                        while (l_bit_pos < bit_end) {           // handle 1-byte reads correctly
                                if (len == 0) {
                                        n_bits = l_n_bits;
                                        maxcode = l_maxcode;
                                        maxmaxcode = l_maxmaxcode;
                                        bitmask = l_bitmask;
                                        oldcode = l_oldcode;
                                        finchar = l_finchar;
                                        stackp = l_stackp;
                                        free_ent = l_free_ent;
                                        bit_pos = l_bit_pos;

                                        return off - start;
                                }

                                // check for code-width expansion

                                if (l_free_ent > l_maxcode) {
                                        int n_bytes = l_n_bits << 3;
                                        l_bit_pos = (l_bit_pos - 1) +
                                                        n_bytes - (l_bit_pos - 1 + n_bytes) % n_bytes;

                                        l_n_bits++;
                                        l_maxcode = (l_n_bits == maxbits) ? l_maxmaxcode :
                                                        (1 << l_n_bits) - 1;

                                        logger.debug("Code-width expanded to ", l_n_bits);

                                        l_bitmask = (1 << l_n_bits) - 1;
                                        l_bit_pos = resetbuf(l_bit_pos);
                                        continue main_loop;
                                }


                                // read next code

                                int pos = l_bit_pos >> 3;
                                int code = (((l_data[pos] & 0xFF) | ((l_data[pos + 1] & 0xFF) << 8) |
                                                ((l_data[pos + 2] & 0xFF) << 16))
                                                >> (l_bit_pos & 0x7)) & l_bitmask;
                                l_bit_pos += l_n_bits;


                                // handle first iteration

                                if (l_oldcode == -1) {
                                        if (code >= 256)
                                                throw new IOException("corrupt input: " + code +
                                                                " > 255");
                                        l_finchar = (byte) (l_oldcode = code);
                                        buf[off++] = l_finchar;
                                        len--;
                                        continue;
                                }


                                // handle CLEAR code

                                if (code == TBL_CLEAR && block_mode) {
                                        System.arraycopy(zeros, 0, l_tab_prefix, 0, zeros.length);
                                        l_free_ent = TBL_FIRST - 1;

                                        int n_bytes = l_n_bits << 3;
                                        l_bit_pos = (l_bit_pos - 1) +
                                                        n_bytes - (l_bit_pos - 1 + n_bytes) % n_bytes;
                                        l_n_bits = INIT_BITS;
                                        l_maxcode = (1 << l_n_bits) - 1;
                                        l_bitmask = l_maxcode;

                                        logger.debug("Code tables reset");

                                        l_bit_pos = resetbuf(l_bit_pos);
                                        continue main_loop;
                                }


                                // setup

                                int incode = code;
                                l_stackp = l_stack.length;


                                // Handle KwK case

                                if (code >= l_free_ent) {
                                        if (code > l_free_ent)
                                                throw new IOException("corrupt input: code=" + code +
                                                                ", free_ent=" + l_free_ent);

                                        l_stack[--l_stackp] = l_finchar;
                                        code = l_oldcode;
                                }


                                // Generate output characters in reverse order

                                while (code >= 256) {
                                        l_stack[--l_stackp] = l_tab_suffix[code];
                                        code = l_tab_prefix[code];
                                }
                                l_finchar = l_tab_suffix[code];
                                buf[off++] = l_finchar;
                                len--;


                                // And put them out in forward order

                                s_size = l_stack.length - l_stackp;
                                int num = (s_size >= len) ? len : s_size;
                                System.arraycopy(l_stack, l_stackp, buf, off, num);
                                off += num;
                                len -= num;
                                l_stackp += num;


                                // generate new entry in table

                                if (l_free_ent < l_maxmaxcode) {
                                        l_tab_prefix[l_free_ent] = l_oldcode;
                                        l_tab_suffix[l_free_ent] = l_finchar;
                                        l_free_ent++;
                                }


                                // Remember previous code

                                l_oldcode = incode;


                                // if output buffer full, then return

                                if (len == 0) {
                                        n_bits = l_n_bits;
                                        maxcode = l_maxcode;
                                        bitmask = l_bitmask;
                                        oldcode = l_oldcode;
                                        finchar = l_finchar;
                                        stackp = l_stackp;
                                        free_ent = l_free_ent;
                                        bit_pos = l_bit_pos;

                                        return off - start;
                                }
                        }

                        l_bit_pos = resetbuf(l_bit_pos);
                } while
                        // old code: (got>0)  fails if code width expands near EOF
                        (got > 0            // usually true
                        || l_bit_pos < (end << 3) - (l_n_bits - 1));  // last few bytes

                n_bits = l_n_bits;
                maxcode = l_maxcode;
                bitmask = l_bitmask;
                oldcode = l_oldcode;
                finchar = l_finchar;
                stackp = l_stackp;
                free_ent = l_free_ent;
                bit_pos = l_bit_pos;

                eof = true;
                return off - start;
        }


        /**
         * Moves the unread data in the buffer to the beginning and resets
         * the pointers.
         */
        private int resetbuf(int bit_pos) {
                int pos = bit_pos >> 3;
                System.arraycopy(data, pos, data, 0, end - pos);
                end -= pos;
                return 0;
        }


        private void fill() throws IOException {
                got = in.read(data, end, data.length - 1 - end);
                if (got > 0) end += got;
        }


        @Override
        public synchronized long skip(long num) throws IOException {
                return Math.max(0, read(new byte[(int) num]));
        }


        @Override
        public synchronized int available() throws IOException {
                if (eof) return 0;
                // the old code was:    return in.available();
                // it fails because this.read() can return bytes 
                // even after in.available()  is zero
                // -- zweibieren
                int avail = in.available(); 
                return (avail == 0) ? 1 : avail;
        }


        static final int LZW_MAGIC = 0x1f9d;
        private static final int MAX_BITS = 16;
        private static final int INIT_BITS = 9;
        private static final int HDR_MAXBITS = 0x1f;
        private static final int HDR_EXTENDED = 0x20;
        private static final int HDR_FREE = 0x40;
        private static final int HDR_BLOCK_MODE = 0x80;

        private void parse_header() throws IOException {
                // read in and check magic number
                int t = in.read();
                if (t < 0) throw new EOFException("Failed to read magic number");
                int magic = (t & 0xff) << 8;
                t = in.read();
                if (t < 0) throw new EOFException("Failed to read magic number");
                magic += t & 0xff;
                if (magic != LZW_MAGIC)
                        throw new IOException("Input not in compress format (read " +
                                        "magic number 0x" +
                                        Integer.toHexString(magic) + ")");

                // read in header byte
                int header = in.read();
                if (header < 0) throw new EOFException("Failed to read header");

                block_mode = (header & HDR_BLOCK_MODE) > 0;
                maxbits = header & HDR_MAXBITS;

                if (maxbits > MAX_BITS)
                        throw new IOException("Stream compressed with " + maxbits +
                                        " bits, but can only handle " + MAX_BITS +
                                        " bits");

                if ((header & HDR_EXTENDED) > 0)
                        throw new IOException("Header extension bit set");

                if ((header & HDR_FREE) > 0)
                        throw new IOException("Header bit 6 set");

                logger.debug("block mode: {}", block_mode);
                logger.debug("max bits:   {}", maxbits);

                // initialize stuff
                maxmaxcode = 1 << maxbits;
                n_bits = INIT_BITS;
                maxcode = (1 << n_bits) - 1;
                bitmask = maxcode;
                oldcode = -1;
                finchar = 0;
                free_ent = block_mode ? TBL_FIRST : 256;

                tab_prefix = new int[1 << maxbits];
                tab_suffix = new byte[1 << maxbits];
                stack = new byte[1 << maxbits];
                stackp = stack.length;

                for (int idx = 255; idx >= 0; idx--)
                        tab_suffix[idx] = (byte) idx;
        }

        /**
         * This stream does not support mark/reset on the stream.
         *
         * @return false
         */
        @Override
        public boolean markSupported() {
                return false;
        }

        /**
         * Read a named file and uncompress it.
         * @param fileInName Name of compressed file.
         * @param out A destination for the result. It is closed after data is sent.
         * @return number of bytes sent to the output stream,
         * @throws IOException for any error
         */
        public static long uncompress(String fileInName, FileOutputStream out) 
                        throws IOException {
                long start = System.currentTimeMillis();
                long total;
                try (InputStream fin = new FileInputStream(fileInName)) {
                        total = uncompress(fin, out);
                }
                out.close();

                if (debugTiming) {
                        long end = System.currentTimeMillis();
                        logger.info("Decompressed {} bytes", total);
                        UncompressInputStream.logger.info("Time: {} seconds", (end - start) / 1000);
                }
                return total;
        }

        /**
        * Read an input stream and uncompress it to an output stream.
        * @param in the incoming InputStream. It is NOT closed.
        * @param out the destination OutputStream. It is NOT closed.
        * @return number of bytes sent to the output stream
        * @throws IOException for any error
        */
        public static long uncompress(InputStream in, OutputStream out) 
                throws IOException {
                UncompressInputStream ucis = new UncompressInputStream(in);
                long total = 0;
                byte[] buffer = new byte[100000];
                while (true) {
                        int bytesRead = ucis.read(buffer);
                        if (bytesRead == -1) break;
                        out.write(buffer, 0, bytesRead);
                        total += bytesRead;
                }
                return total;
        }

        private static final boolean debugTiming = false;

        /**
         * Reads a file, uncompresses it, and sends the result to stdout.
         * Also writes trivial statistics to stderr.
         * @param args An array with one String element, the name of the file to read.
         * @throws IOException for any failure
         */
        public static void main(String[] args) throws Exception {
                if (args.length != 1) {
                        logger.info("Usage: UncompressInputStream <file>");
                        System.exit(1);
                }
                long beg = System.currentTimeMillis();

                long tot;
                try (InputStream in = new FileInputStream(args[0])) {
                        tot = uncompress(in, System.out);
                }

                long end = System.currentTimeMillis();
                logger.info("Decompressed {} bytes", tot);
                logger.info("Time: {} seconds", (end - beg) / 1000);
        }
}