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 Modest v. Korff
   */
  
  package com.actelion.research.chem.descriptor.flexophore;
  
  import com.actelion.research.chem.descriptor.DescriptorEncoder;
  import com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore;
  import com.actelion.research.util.datamodel.IntVec;
  
  import java.nio.charset.StandardCharsets;
  
  public class MolDistHistEncoder {
  	
  	private static MolDistHistEncoder INSTANCE;
  
  	private DistHistEncoder distHistEncoder;
  	
  	public MolDistHistEncoder() {
  		
  		distHistEncoder = new DistHistEncoder();
  		
  	}
  	
  	public String encode(MolDistHist mdh){
  		
  		if(!mdh.isFinalized())
  			mdh.realize();
  				
  		String strNodes = encodeByteVec(mdh.getArrNode());
  				
  		String strDistHist = " " + distHistEncoder.encodeHistograms(mdh);
  
  		String atoms = mdh.getNodeAtoms() == null ? "" : " " + new String(new DescriptorEncoder().encodeIntArray2D(mdh.getNodeAtoms()), StandardCharsets.UTF_8);
  		
  		return strNodes + strDistHist + atoms;
  	}
  	
  	public MolDistHist decode(byte [] arr){
  		return decode(new String(arr, StandardCharsets.UTF_8));
  	}
  	
  	public MolDistHist decode(String s){
  
  		if(s.equals(DescriptorHandlerFlexophore.FAILED_STRING)){
  			return DescriptorHandlerFlexophore.FAILED_OBJECT;
  		}
  		
  		String[] st = s.split(" ");
  		
  		byte [] arrNodes = decodeNodes(st[0]);
  
  		int nNodes=0;
  		int pos=0;
  		while(arrNodes[pos] > 0){
  			pos += arrNodes[pos] * PPNode.getNumBytesEntry() + 1;
  			
  			nNodes++;
  			
  			if(pos >= arrNodes.length){
  				break;
  			}
  		}
  
  		byte [] arrNodesTrunc = new byte [pos];
  		
  		System.arraycopy(arrNodes, 0, arrNodesTrunc, 0, arrNodesTrunc.length);
  				
  		MolDistHist mdh = new MolDistHist(nNodes);
  				
  		mdh.setArrNode(arrNodesTrunc);
  		
  		if(st.length >= 2 && st[1].length() != 0)
  			distHistEncoder.decodeHistograms(st[1], mdh);
  
  		if (st.length >= 3)
  			mdh.setNodeAtoms(new DescriptorEncoder().decodeIntArray2D(st[2].getBytes(StandardCharsets.UTF_8)));
  
  		return mdh;
  
  	}
  	
  	/**
  	 * 
  	 * @param s
  	 * @return
  	 */
  	public static byte [] decodeNodes(String s){
  		
  		IntVec iv = new IntVec(new DescriptorEncoder().decode(s));
  		
  		byte [] arr = new byte [iv.sizeBytes()];
  		
  		int sum=0;
  		for (int i = 0; i < arr.length; i++) {
  			arr[i] = (byte)(iv.getByte(i) & 0xFF);
  			sum += Math.abs(arr[i]);	
  		}
  		
  		if(sum==0){
  			throw new RuntimeException("Node vector contains only 0's!");
  		}
  		
  		return arr;
  	}
  
  	public static MolDistHistEncoder getInstance(){
  		
  		if(INSTANCE == null){
  			INSTANCE = new MolDistHistEncoder();
  		}
  		
  		return INSTANCE;
  	}
  
  	private static String encodeByteVec(byte [] arr){
  		
  		double ratio = Integer.SIZE / Byte.SIZE;
  		int sizeIntVec = (int)((arr.length / ratio) + ((ratio-1) / ratio));
  		IntVec iv = new IntVec(sizeIntVec);
  		for (int i = 0; i < arr.length; i++) {
  			iv.setByte(i, (arr[i] & 0xFF));
  		}
  		String s= new String (new DescriptorEncoder().encode(iv.get()));
  		
  		return s;
  	}
  	
  
  
  }
  