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 Thomas Sander
   */
  
  package com.actelion.research.chem;
  
  import com.actelion.research.util.DoubleFormat;
  
  public class Mutation {
      public static final int MUTATION_ADD_ATOM = 1;
      public static final int MUTATION_INSERT_ATOM = 2;
      public static final int MUTATION_CHANGE_ATOM = 4;
      public static final int MUTATION_CUTOUT_ATOM = 8;
      public static final int MUTATION_DELETE_ATOM = 16;
      public static final int MUTATION_CLOSE_RING = 32;
      public static final int MUTATION_CHANGE_BOND = 64;
      public static final int MUTATION_DELETE_BOND = 128;
      public static final int MUTATION_CHANGE_RING = 256;
  	public static final int MUTATION_CLOSE_RING_AND_AROMATIZE = 512;
  	public static final int MUTATION_TOGGLE_AMID_SULFONAMID = 1024;
      public static final int MUTATION_MIGRATE = 2048;
      public static final int MUTATION_SWAP_SUBSTITUENT = 4096;
      public static final int MUTATION_DELETE_SUBSTITUENT = 8192;
      public static final int MUTATION_CUTOUT_SFRAGMENT = 16384;
  	public static final int MUTATION_INVERT_PARITY = 32768;
  
  	public static final int[][] cAllowedAtomicNo = 
  		{ { 5, 6, 7, 8, 9, 15, 16, 17, 35, 53 },
  		  { 6, 7, 8, 15, 16 },
  		  { 6, 7 } };
  
  	public int mMutationType;
  	public int mWhere1;
      public int mWhere2;
  	public int mSpecifier1;
  	public int mSpecifier2;
  	public int[] mAtomList;
  	public double mProbability;
  
  	public Mutation() {
  		}
  
  	public Mutation(int mutationType,
  	                int where1, int where2,
  	                int specifier1, int specifier2,
  	                double probability) {
  		mMutationType	= mutationType;
  		mWhere1			= where1;
          mWhere2         = where2;
  		mSpecifier1		= specifier1;
  		mSpecifier2		= specifier2;
  		mProbability = probability;
  		}
  
  	public Mutation(int mutationType, int where1, int where2, int specifier1, int[] atomList,
  					double probability) {
  		mMutationType	= mutationType;
  		mWhere1			= where1;
  		mWhere2         = where2;
  		mSpecifier1		= specifier1;
  		mAtomList		= atomList;
  		mProbability = probability;
  	}
  
  	public String toString() {
          switch (mMutationType) {
          case MUTATION_ADD_ATOM:
              return "Atom Addition; AtAtom:"+mWhere1
                    +" AtomicNo:"+mSpecifier1
                    +" BondType:"+mSpecifier2
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_INSERT_ATOM:
              return "Atom Insertion; AtBond:"+mWhere1
                    +" AtomicNo:"+mSpecifier1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_CHANGE_ATOM:
              return "Atom Change; Atom:"+mWhere1
                    +" AtomicNo:"+mSpecifier1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_DELETE_ATOM:
              return "Atom Deletion; Atom:"+mWhere1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_CUTOUT_ATOM:
              return "Atom CutOut; Atom:"+mWhere1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_CLOSE_RING:
              return "Bond Addition; FromAtom:"+mWhere1
                    +" ToAtom:"+mWhere2
                    +" BondType:"+mSpecifier1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_CHANGE_BOND:
              return "Bond Change; Bond:"+mWhere1
                    +" BondType:"+mSpecifier1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_DELETE_BOND:
              return "Bond Deletion; Bond:"+mWhere1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_CHANGE_RING:
              return "Ring Change; Ring:"+mWhere1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
  		case MUTATION_CLOSE_RING_AND_AROMATIZE:
  			return "Close Ring And Aromatize; FromAtom:"+mWhere1
  				  +" ToAtom:"+mWhere2
  				  +" Probability:"+DoubleFormat.toString(mProbability);
  		case MUTATION_TOGGLE_AMID_SULFONAMID:
  			return "Toggle Amid-Sulfonamid; Atom:"+mWhere1
  				  +" Oxygen:"+mWhere1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_MIGRATE:
              return "Group Migration; Bond:"+mWhere1
                    +" originalAtom:"+mSpecifier1
                    +" newAtom:"+mSpecifier2
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_SWAP_SUBSTITUENT:
              return "Swap Substituent; coreAtom1:"+mWhere1
                    +" firstAtom1:"+mSpecifier1
                    +" coreAtom2:"+mWhere2
                    +" firstAtom2:"+mSpecifier2
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_DELETE_SUBSTITUENT:
              return "Delete Substituent; coreAtom:"+mWhere1
                    +" firstAtom:"+mSpecifier1
  				  +" Probability:"+DoubleFormat.toString(mProbability);
          case MUTATION_CUTOUT_SFRAGMENT:
              return "CutOut Fragment; rootAtom:"+mWhere1
                    +" new bond from atom1:"+mSpecifier1+" to atom2:"+mSpecifier2
  				  +" Probability:"+DoubleFormat.toString(mProbability);
  	        case MUTATION_INVERT_PARITY:
  	        return "Invert Parity; "
  			      +(mWhere1 != -1 ? "atom:"+mWhere1 : "bond:"+mWhere2)
  		          +" Probability:"+DoubleFormat.toString(mProbability);
              }
          return "Unknown Mutation";
          }
      }