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.chem.properties.complexity;
  
  import java.io.IOException;
  import java.io.InputStream;
  
  public class BitArray128 extends IndexHash implements IBitArray {
  
  	public static final int HASH_NOT_SET=-1;
  	public static final int HASH_SIDE_STEP =-2;
  
  	// Two long
  	public static final int MAX_NUM_BITS = 128;
  	
  	
  	// Each bit represents one bond
  	long l1;
  	long l2;
  
  	// bit index after the last bit set
  	protected char sizeAfterLastBitSet;
  
  	/**
  	 * 
  	 */
  	public BitArray128() {
  		sizeAfterLastBitSet = 0;
  	}
  	
  	public BitArray128(int index) {
  		super(index);
  	}
  	
  	/**
  	 * Deep copy
  	 * @param f
  	 */
  	public BitArray128(BitArray128 f) {
  		copyIntoThis(f);
  	}
  	
  	/**
  	 * Deep copy
  	 * The index is not copied
  	 * @param orign
  	 */
  	public void copyIntoThis(IBitArray orign) {
  		
  		BitArray128 ba = (BitArray128)orign;
  		
  		setHash(ba.hash);
  		
  		l1 = ba.l1;
  		
  		l2 = ba.l2;
  		
  	}
  	
  	@Override
  	public boolean equals(Object obj) {
  		
  		if(!(obj instanceof BitArray128)){
  			return false;
  		}
  		
  		BitArray128 f = (BitArray128)obj;
  		
  		if(l1 != f.l1) {
  			return false;
  		} else if(l2 != f.l2){
  			return false;
  		}
  		
  		return true;
  		
  	}
  	
  	public void add(IBitArray f){
  		int size = f.getSizeAfterLastBitSet();
  		
  		for (int i = 0; i < size; i++) {
  			if(f.isBitSet(i)){
  				setBit(i);
  			}
  		}
  	}
  	
  	public boolean isBitSet(int i) {
      	boolean set=false;
      	
      	int indInInt = Long.SIZE - 1 - (i % Long.SIZE);
      	
          long mask = 1;
          
          mask = mask << indInInt;
          
      	if(i < Long.SIZE) {
      		if((l1 & mask) != 0)
      			set = true;
      	} else {
     		 	if((l2 & mask) != 0)
     		 		set = true;
      	}
          
          return set;
          
      }
  	
      public void setBit(int i) {
      	
      	int indInInt = Long.SIZE - 1 - (i % Long.SIZE);
      	
      	long mask = 1;
          
          mask = mask << indInInt;
          
      	if(i < Long.SIZE) {
      		l1 = l1 | mask;
      	} else {
      		l2 = l2 | mask;
      	}
      	
      	setHash(BitArray128.HASH_NOT_SET);
      	
      	if(i >= sizeAfterLastBitSet){
      		sizeAfterLastBitSet = (char)(i + 1);
      	}
      }
      
      public void unsetBit(int i) {
      	
      	int indInInt = Long.SIZE - 1 - (i % Long.SIZE);
      	
      	long mask = 1;
          
          mask = mask << indInInt;
          
      	if(i < Long.SIZE) {
      		l1 = l1 & ~mask;
      	} else {
      		l2 = l2 & ~mask;
      	}
      	
      	setHash(BitArray128.HASH_NOT_SET);
      	
      	if((i+1) == sizeAfterLastBitSet){
      		sizeAfterLastBitSet = 0;
      		for (int j = i; j >= 0; j++) {
      			if(isBitSet(j)){
      				sizeAfterLastBitSet = (char)(j + 1);
      			}
  			}
      	}
      	
      }
      
      public boolean isOverlap(IBitArray f) {
  		boolean overlap=false;
  		
  		final int size = f.getSizeAfterLastBitSet();
  		
  		for (int i = 0; i < size; i++) {
  			if(isBitSet(i) && f.isBitSet(i)){
  				overlap=true;
  				break;
  			}
  		}
  		
  		return overlap;
  	}
      
      public int getBitsSet(){
      	int bits=0;
      	
      	int size = getSizeAfterLastBitSet();
      	
      	for (int i = 0; i < size; i++) {
      		if(isBitSet(i)){
      			bits++;
      		}
      	}
      	
      	return bits;
      }
      
      /**
  	 * @return the sizeAfterLastBitSet
  	 */
  	public int getSizeAfterLastBitSet() {
  		return sizeAfterLastBitSet;
  	}
  
  	public void reset() {
      	
  		setHash(BitArray128.HASH_NOT_SET);
  
      	l1 = 0;
      	l2 = 0;
      	
  		sizeAfterLastBitSet = 0;
      }
      
      /**
  	 * @return the l1
  	 */
  	public long getL1() {
  		return l1;
  	}
  
  	/**
  	 * @param l1 the l1 to set
  	 */
  	public void setL1(long l1) {
  		this.l1 = l1;
  	}
  
  	/**
  	 * @return the l2
  	 */
  	public long getL2() {
  		return l2;
  	}
  
  	/**
  	 * @param l2 the l2 to set
  	 */
  	public void setL2(long l2) {
  		this.l2 = l2;
  	}
  
  	@Override
  	public String toString() {
  		return toStringBinary();
  	}
  	
  	public String toStringBinary() {
          StringBuilder sb = new StringBuilder();
          
          sb.append(toStringBinary(l1));
          sb.append(toStringBinary(l2));
          
          return sb.toString();
      }
  
  	private static String toStringBinary(long v) {
  		
  		StringBuilder sb = new StringBuilder();
  		
  		int len = Long.SIZE;
  
  		for (int i = 0; i < len; i++) {
  			if ((v & 1) == 1) {
  				sb.insert(0, "1");
  			} else {
  				sb.insert(0, "0");
  			}
  			
  			
  			v = v >> 1;
  		}
  
  		return sb.toString().trim();
  	}
  	
      public static BitArray128 read(InputStream s) throws IOException{
      	    	
      	BitArray128 f = new BitArray128();
      	
      	f.setIndex((int)parseLong(s));
      	
      	f.setHash((int)parseLong(s));
      	
      	f.l1 =  parseLong(s);
      	
      	f.l2 =  parseLong(s);
      	
      	f.sizeAfterLastBitSet =  (char)parseLong(s);
      	
      	return f;
      	
      }
  
      public String write2String() {
      	
      	StringBuilder sb = new StringBuilder();
  
      	sb.append(getIndex());
      	
      	sb.append(" ");
      	
      	sb.append(hashCode());
      	
      	sb.append(" ");
      	
      	sb.append(l1);
      	
      	sb.append(" ");
      	
      	sb.append(l2);
      	
      	sb.append(" ");
      	
      	sb.append(sizeAfterLastBitSet);
      	
      	return sb.toString();
      	
      }
      
      public static long parseLong(InputStream s) throws IOException{
      	
      	int i = -1;
      	StringBuilder sb = new StringBuilder();
      	while(' ' != (i=s.read())){
      		
      		if(i==-1){
      			break;
      		}
      		
      		sb.append((char)i); 
      	}
      	
      	long val = Long.parseLong(sb.toString());
      	
      	return val;
      }
  
  }
  