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.
   *
   * @author Modest v. Korff
   */
  
  package com.actelion.research.chem.descriptor.flexophore;
  
  import com.actelion.research.calc.ArrayUtilsCalc;
  import com.actelion.research.chem.*;
  import com.actelion.research.chem.descriptor.DescriptorEncoder;
  
  import java.nio.charset.StandardCharsets;
  import java.util.ArrayList;
  import java.util.HashSet;
  import java.util.List;
  import java.util.StringTokenizer;
  
  public class MolDistHistVizEncoder {
  	
  	public static final String SEP = "-1";
  	
  	
  	private static MolDistHistVizEncoder INSTANCE;
  	
  	private MolDistHistEncoder molDistHistEncoder;
  
  	/**
  	 * 
  	 */
  	public MolDistHistVizEncoder() {
  		molDistHistEncoder = new MolDistHistEncoder();
  	}
  	
  	/**
  	 * 
  	 * @param vizinfo String with content generated by toStringVizInfoEncoded(). 
  	 * @param flexophore the encoded descriptor
  	 * @return
  	 */
  	public MolDistHistViz readEncoded(String vizinfo, String flexophore){
  		
  		StringTokenizer st = new StringTokenizer(vizinfo);
  		
  		String idcode = st.nextToken();
  		String coord = st.nextToken();
  				
  		MolDistHist mdh = molDistHistEncoder.decode(flexophore);
  		
  		IDCodeParser parser = new IDCodeParser();
  		
  		StereoMolecule ster = parser.getCompactMolecule(idcode, coord);
  		ster.ensureHelperArrays(StereoMolecule.cHelperRings);
  		
  		int cc=0;
  		List<PPNodeViz> liPPNodeViz = new ArrayList<PPNodeViz>();
  		
  		boolean hasInevitablePPPoints = false;
  		while(st.hasMoreTokens()){
  			
  			String sArr = st.nextToken();
  			
  			if(sArr.equals(SEP)){
  				hasInevitablePPPoints = true;
  				break;
  			}
  			
  			int [] arrAtIndex = ArrayUtilsCalc.readIntArray(sArr);
  			
  			PPNodeViz node = new PPNodeViz(mdh.getNode(cc));
  			
  			Coordinates [] arrCoordinates = new Coordinates [arrAtIndex.length];
  			for (int i = 0; i < arrAtIndex.length; i++) {
  				
  				double x = ster.getAtomX(arrAtIndex[i]);
  				double y = ster.getAtomY(arrAtIndex[i]);
  				double z = ster.getAtomZ(arrAtIndex[i]);
  				arrCoordinates[i] = new Coordinates(x, y, z);
  				node.addIndexOriginalAtom(arrAtIndex[i]);
  			}
  
  			Coordinates coordCenter = Coordinates.createBarycenter(arrCoordinates);
  			node.setCoordinates(coordCenter.x, coordCenter.y, coordCenter.z);
  			
  			liPPNodeViz.add(node);
  			cc++;
  		}
  		
  		Molecule3D ff = new Molecule3D(ster);
  		for (int i = 0; i < ff.getAllAtoms(); i++) {
  			
  			Coordinates c = new Coordinates(ster.getAtomX(i), ster.getAtomY(i), ster.getAtomZ(i));
  			
  			ff.setCoordinates(i, c);
  		}
  		
  		MolDistHistViz mdhv = new MolDistHistViz(mdh.getNumPPNodes(), ff);
  		for (int i = 0; i < mdh.getNumPPNodes(); i++) {
  			mdhv.addNode(liPPNodeViz.get(i));
  		}
  		
  		for (int i = 0; i < mdh.getNumPPNodes(); i++) {
  			for (int j = i+1; j < mdh.getNumPPNodes(); j++) {
  				mdhv.setDistHist(i, j, mdh.getDistHist(i, j));
  			}
  		}
  		
  		if(hasInevitablePPPoints) {
  			
  			String strInevitablePPPoints = st.nextToken();
  			
  			DescriptorEncoder de = new DescriptorEncoder();
  
  			byte [] arrIndexInevitablePPPoints = de.decodeCounts(strInevitablePPPoints);
  			
  			for (int i = 0; i < arrIndexInevitablePPPoints.length; i++) {
  				mdhv.addMandatoryPharmacophorePoint(arrIndexInevitablePPPoints[i]);
  			}
  			
  		}
  		
  		mdhv.realize();
  		
  		return mdhv;
  		
  	}
  	
  	/**
  	 * Encodes the structure information, that it can be written to an DWAR file. 
  	 * The atom indices from the structure are mapped on the nodes 
  	 * under consideration of the changed indices generated by the Canonizer.
  	 * H atoms are not covered by the indices generated by the Canonizer. We take simply the old indices and hope the best.
  	 * @return A String with: idcode coordinates [int array]n for each PPNode an int array is written, 
  	 * it contains the indices of the mapping atoms in the idcode.  
  	 */
  	public static String toStringVizInfoEncoded(MolDistHistViz mdhv) {
  
  		StringBuilder sb = new StringBuilder();
  		
  		if(mdhv.molecule3D == null)
  			return null;
  		
  		Molecule3D molecule3D = MolDistHistViz.finalizeMolecule(mdhv.molecule3D);
  
  		List<List<Integer>> liliOriginalIndex = new ArrayList<List<Integer>>();
  		for(int i=0; i < mdhv.getNumPPNodes(); i++){
  			PPNodeViz node = mdhv.getNode(i);
  			List<Integer> liOriginalIndex = node.getListIndexOriginalAtoms();
  			liliOriginalIndex.add(liOriginalIndex);
  		}
  		
  		StereoMolecule mol = new Molecule3D(molecule3D);
  		
  		mol.ensureHelperArrays(Molecule.cHelperRings);
  		
  
  		Canonizer can = new Canonizer(mol);
  		
  		String idcode = can.getIDCode();
  		
  		String coord = can.getEncodedCoordinates(true);
  		
  		int [] arrMap = can.getGraphIndexes();
  
  		int nNonHAtoms = mol.getAtoms();
  		
  		for (int i = 0; i < liliOriginalIndex.size(); i++) {
  			List<Integer> liOriginalIndex = liliOriginalIndex.get(i);
  			for (int j = 0; j < liOriginalIndex.size(); j++) {
  				int ind = liOriginalIndex.get(j);
  				try {
  					if(ind<nNonHAtoms) {
  						liOriginalIndex.set(j, arrMap[ind]);
  					} else { // For the H atoms we hope the best.
  						liOriginalIndex.set(j, ind);
  					}
  				} catch (Exception e) {
  					e.printStackTrace();
  				}
  			}
  		}
  		
  		sb.append(idcode);
  		sb.append(" ");
  		sb.append(coord);
  		sb.append(" ");
  		for (int i = 0; i < liliOriginalIndex.size(); i++) {
  			sb.append(ArrayUtilsCalc.toString(liliOriginalIndex.get(i)));
  			if(i<liliOriginalIndex.size()-1)
  				sb.append(" ");
  		}
  		
  		HashSet<Integer> hsIndexInevitablePPPoints = mdhv.getHashSetIndexInevitablePPPoints();
  		
  		if(hsIndexInevitablePPPoints.size() > 0)  {
  			
  			sb.append(" " + SEP + " ");
  			
  			DescriptorEncoder de = new DescriptorEncoder();
  			
  			byte [] a = new byte [hsIndexInevitablePPPoints.size()];
  			
  			int cc=0;
  			for (int index : hsIndexInevitablePPPoints) {
  				a[cc++]=(byte)index;
  			}
  			
  			String strEncodedInevitablePPPoints = new String(de.encodeCounts(a), StandardCharsets.UTF_8);
  			
  			sb.append(strEncodedInevitablePPPoints);
  		}
  		
  		return sb.toString();
  	}
  	
  	public static MolDistHistVizEncoder getInstance(){
  		
  		if(INSTANCE == null){
  			INSTANCE = new MolDistHistVizEncoder();
  		}
  		
  		return INSTANCE;
  	}
  
  
  }
  