content: /*
  * Copyright (c) 1997 - 2016
  * Actelion Pharmaceuticals Ltd.
  * Gewerbestrasse 16
  * CH-4123 Allschwil, Switzerland
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  *
  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
  * 3. Neither the name of the the copyright holder nor the
  *    names of its contributors may be used to endorse or promote products
  *    derived from this software without specific prior written permission.
  *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
  * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
  * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
  */
  
  package com.actelion.research.util;
  
  import java.io.*;
  
  public class BinaryDecoder {
  	private BufferedReader	mReader;
  	private int				mAvailableBufferBits,mData,mDataBitCount,
  							mBitsPerCharacter,mBaseCharacter;
  	private int[]			mMask;
  
  	/**
  	 * Convenience method to directly decode a String-encoded byte array.
  	 * @param encodedBytes
  	 * @param dataBitCount count of bits per byte
  	 * @return
  	 */
  	public static byte[] toBytes(String encodedBytes, int dataBitCount) {
  		BinaryDecoder decoder = new BinaryDecoder(new BufferedReader(new StringReader(encodedBytes)));
  		try {
  			byte[] data = new byte[decoder.initialize(dataBitCount)];
  			for (int i=0; i<data.length; i++)
  				data[i] = (byte)decoder.read();
  			return data;
  			} catch (IOException ioe) {}
  		return null;
  		}
  
  	/**
  	 * Convenience method to directly decode a String-encoded int array.
  	 * @param encodedBytes
  	 * @param dataBitCount count of bits per byte
  	 * @return
  	 */
  	public static int[] toInts(String encodedBytes, int dataBitCount) {
  		BinaryDecoder decoder = new BinaryDecoder(new BufferedReader(new StringReader(encodedBytes)));
  		try {
  			int[] data = new int[decoder.initialize(dataBitCount)];
  			for (int i=0; i<data.length; i++)
  				data[i] = decoder.read();
  			return data;
  			} catch (IOException ioe) {}
  		return null;
  		}
  
  	public BinaryDecoder(BufferedReader reader) {
  		this(reader, 6, 64);
  		}
  
  	public BinaryDecoder(BufferedReader reader, int bitsPerCharacter, int baseCharacter) {
  		mReader = reader;
  		mBitsPerCharacter = bitsPerCharacter;
  		mBaseCharacter = baseCharacter;
  		mAvailableBufferBits = 0;
  
  		mMask = new int[bitsPerCharacter+1];
  		for (int i=1; i<=bitsPerCharacter; i++)
  			mMask[i] = (mMask[i-1] << 1) | 1;
  		}
  
  	public int initialize(int dataBitCount) throws IOException {
  		mDataBitCount = 32;
  		int totalByteCount = read();
  		mDataBitCount = dataBitCount;
  		return totalByteCount;
  		}
  
  	public int read() throws IOException {
  		int data = 0;
  		int neededBits = mDataBitCount;
  		while (neededBits != 0) {
  			if (mAvailableBufferBits == 0) {
  				while ((mData = mReader.read() - mBaseCharacter) < 0);
  				mAvailableBufferBits = mBitsPerCharacter;
  				}
  			int bitsToRead = Math.min(mAvailableBufferBits, neededBits);
  			int dataBits = mData & (mMask[bitsToRead] << (mAvailableBufferBits - bitsToRead));
  			data |= (mAvailableBufferBits > neededBits) ?
  						dataBits >> (mAvailableBufferBits - neededBits)
  					  : dataBits << (neededBits - mAvailableBufferBits);
  			neededBits -= bitsToRead;
  			mAvailableBufferBits -= bitsToRead;
  			}
  		return data;
  		}
  	}
  