content: /*
   * Copyright (c) 1997 - 2022
   * Idorsia Pharmaceuticals Ltd.
   * Hegenheimermattweg 91
   * 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 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.
   *
   * @author Thomas Sander
   */
  
  package com.actelion.research.util;
  
  import java.io.BufferedWriter;
  import java.io.IOException;
  import java.io.StringWriter;
  
  public class BinaryEncoder {
  	private BufferedWriter	mWriter;
  	private int				mFreeBufferBits,mData,mCharsWritten,mDataBitCount,
  							mBitsPerCharacter,mBaseCharacter,mLineLength;
  	private int[]			mMask;
  
  	/**
  	 * Convenience method to directly encode an int array into a String
  	 * Uses 6 bits per character using 64 characters from '@' (ASCII 64).
  	 * @param data
  	 * @param dataBitCount
  	 * @return
  	 */
  	public static String toString(int[] data, int dataBitCount) {
  		StringWriter writer = new StringWriter();
  		BinaryEncoder encoder = new BinaryEncoder(new BufferedWriter(writer));
  		try {
  			encoder.initialize(dataBitCount, data.length);
  			for (int d:data)
  				encoder.write(d);
  			encoder.finish();
  			} catch (IOException ioe) {}
  		return writer.toString();
  		}
  
  	/**
  	 * Convenience method to directly encode a byte array into a String
  	 * Uses 6 bits per character using 64 characters from '@' (ASCII 64).
  	 * @param data
  	 * @param dataBitCount
  	 * @return
  	 */
  	public static String toString(byte[] data, int dataBitCount) {
  		StringWriter writer = new StringWriter();
  		BinaryEncoder encoder = new BinaryEncoder(new BufferedWriter(writer));
  		try {
  			encoder.initialize(dataBitCount, data.length);
  			for (int d:data)
  				encoder.write(d);
  			encoder.finish();
  			} catch (IOException ioe) {}
  		return writer.toString();
  		}
  
  	/**
  	 * Creates an encoder to make a BufferedWriter write byte/int arrays as Strings.
  	 * This version uses 6 bits per character using 64 characters from '@' (ASCII 64).
  	 * It inserts a platform specific newline/linefeed after every 80 characters.
  	 * @param writer
  	 */
  	public BinaryEncoder(BufferedWriter writer) {
  		this(writer, 6, 64, 80);
  		}
  
  	/**
  	 * Instantiates an encoder for byte/int arrays to String.
  	 * @param writer
  	 * @param bitsPerCharacter no of bits to be used per character
  	 * @param baseCharacter lowest character, which encodes value '0'
  	 * @param lineLength -1 (no LF/NL) or count of character after which a NL/LF is inserted
  	 */
  	public BinaryEncoder(BufferedWriter writer, int bitsPerCharacter,
  									  int baseCharacter, int lineLength) {
  		mWriter = writer;
  		mBitsPerCharacter = bitsPerCharacter;
  		mBaseCharacter = baseCharacter;
  		mLineLength = lineLength;
  		mData = 0;
  		mCharsWritten = 0;
  		mFreeBufferBits = bitsPerCharacter;
  
  		mMask = new int[bitsPerCharacter+1];
  		for (int i=1; i<=bitsPerCharacter; i++)
  			mMask[i] = (mMask[i-1] << 1) | 1;
  		}
  
  	/**
  	 * Initializes encoder for writing one binary array
  	 * @param dataBitCount count of bits to be written per data value
  	 * @param totalByteCount count of data values to be encoded
  	 * @throws IOException
  	 */
  	public void initialize(int dataBitCount, int totalByteCount) throws IOException {
  		mDataBitCount = 32;
  		write(totalByteCount);
  		mDataBitCount = dataBitCount;
  		}
  
  	/**
  	 * Encodes and writes one data value
  	 * @param data
  	 * @throws IOException
  	 */
  	public void write(int data) throws IOException {
  		int remainingSourceBits = mDataBitCount;
  		while (remainingSourceBits != 0) {
  			int bitsToWrite = Math.min(mFreeBufferBits, remainingSourceBits);
  			int dataBits = data & (mMask[bitsToWrite] << (remainingSourceBits - bitsToWrite));
  			mData |= (remainingSourceBits > mFreeBufferBits) ?
  						dataBits >> (remainingSourceBits - mFreeBufferBits)
  					  : dataBits << (mFreeBufferBits - remainingSourceBits);
  			remainingSourceBits -= bitsToWrite;
  			mFreeBufferBits -= bitsToWrite;
  			if (mFreeBufferBits == 0) {
  				mWriter.write(mBaseCharacter+mData);
  				mFreeBufferBits = mBitsPerCharacter;
  				mData = 0;
  				mCharsWritten++;
  				if (mLineLength != -1 && (mCharsWritten % mLineLength == 0))
  					mWriter.newLine();
  				}
  			}
  		}
  
  	/**
  	 * Writes remaining bits from buffer, if there are any and possibly adds final NL/LF.
  	 */
  	public void finish() throws IOException {
  		if (mFreeBufferBits < mBitsPerCharacter) {
  			mWriter.write(mBaseCharacter+mData);
  			if (mLineLength != -1)
  				mWriter.newLine();
  			}
  		else if (mLineLength != -1 && (mCharsWritten % mLineLength != 0)) {
  			mWriter.newLine();
  			}
  		mWriter.flush();
  		}
  	}
  