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 FragmentDefinedByBondsIdCode implements Comparable<FragmentDefinedByBondsIdCode> {
  
  	
  	String idcode;
  	
  	private int frequency;
  
  	private IBitArray bitArray;
  	
  	public FragmentDefinedByBondsIdCode() {
  		idcode = "";
  	}
  	
  	public FragmentDefinedByBondsIdCode(IBitArray f) {
  		this.bitArray = f;
  	}
  	
  	public FragmentDefinedByBondsIdCode(FragmentDefinedByBondsIdCode f) {
  		this.bitArray = f.bitArray;
  		idcode = f.idcode;
  		frequency = f.frequency;
  		
  	}
  
  	public void addBits(IBitArray ba){
  		this.bitArray.add(ba);
  	}
  	
  	/**
  	 * @return the idcode
  	 */
  	public String getIdCode() {
  		return idcode;
  	}
  
  	public IBitArray getBitArray(){
  		return bitArray;
  	}
  	
  	/**
  	 * @param idcode the idcode to set
  	 */
  	public void setIdCode(String idcode) {
  		this.idcode = idcode;
  	}
  	
  	public int getFrequency() {
  		return frequency;
  	}
  
  	public void incrementFrequency() {
  		this.frequency++;
  	}
  	
  	public void setFrequency(int frequency) {
  		this.frequency = frequency;
  	}
  
  	public int getBitsSet() {
  		if(bitArray==null){
  			return 0;
  		}
  		
  		return bitArray.getBitsSet();
  	}
  	
  	public boolean isOverlappingBits(IBitArray ba){
  		return bitArray.isOverlap(ba);
  	}
  	
      public String write2String() throws IOException{
      	
      	StringBuilder sb = new StringBuilder();
      	
      	sb.append(idcode);
      	
      	sb.append("\t");
      	
      	sb.append(frequency);
      	
      	sb.append(" ");
  
      	sb.append(bitArray.write2String());
      	
      	return sb.toString();
      	
      }
  
      public static FragmentDefinedByBondsIdCode read(InputStream s) throws IOException{
      	
      	String idcode = parseString(s);
  
      	int frequency = (int) BitArray128.parseLong(s);
      	
      	IBitArray f = BitArray128.read(s);
      	
      	FragmentDefinedByBondsIdCode fIdCode = new FragmentDefinedByBondsIdCode(f);
      	
      	fIdCode.idcode = idcode;
      	
      	fIdCode.frequency = frequency;
      	
      	return fIdCode;
      	
      }
      
      public static String parseString(InputStream s) throws IOException{
      	
      	int i = -1;
      	StringBuilder sb = new StringBuilder();
      	while('\t' != (i=s.read())){
      		sb.append((char)i); 
      	}
      	    	
      	return sb.toString();
      }
  
  
  	@Override
  	public int compareTo(FragmentDefinedByBondsIdCode o) {
  
  		if(idcode==null && o.idcode==null)
  			return 0;
  		else if(o.idcode==null)
  			return 1;
  		else if(idcode==null)
  			return -1;
  
  		return idcode.compareTo(o.idcode);
  	}
  }
  