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.reaction;
  
  import java.io.Serializable;
  
  public class ReactionSearchSpecification implements Serializable {
      static final long serialVersionUID = 0x20200823;
  
  	private static final int TYPE_MASK				= 0x0000FF;
  	public static final int TYPE_NO_REACTION 		= 0x000000; // no structure search (other criteria only)
  	public static final int TYPE_SUBREACTION        = 0x000001;
  	public static final int TYPE_SIMILARITY			= 0x000002;
  	public static final int TYPE_RETRON 			= 0x000003;
  	public static final int TYPE_EXACT_STRICT		= 0x000004;
  	public static final int TYPE_EXACT_NO_STEREO	= 0x000005;
  
  	private int mSearchType;
  	private String[] mQuery;
  	private long[][] mReactionDescriptor,mReactantDescriptor,mProductDescriptor,mRetronDescriptor;
  	private float mReactionCenterSimilarity,mPeripherySimilarity;
  
  	/**
  	 * Creates a complete specification for a reaction similarity search
  	 * with one or more query reactions.
  	 * @param searchType one of TYPE_...
  	 * @param query list of encoded query reactions
  	 * @param reactionDescriptor null or query reaction descriptors
  	 * @param reactantDescriptor null or reactant FFP512 descriptors
  	 * @param productDescriptor null or product FFP512 descriptors
  	 * @param reactionCenterSimilarity in case of TYPE_SIMILARITY
  	 * @param peripherySimilarity in case of TYPE_SIMILARITY
  	 */
  	public ReactionSearchSpecification(int searchType, String[] query,
  	                                   long[][] reactionDescriptor, long[][] reactantDescriptor, long[][] productDescriptor,
  	                                   float reactionCenterSimilarity, float peripherySimilarity) {
  		mSearchType = searchType;
  		mQuery = query;
  		mReactionDescriptor = reactionDescriptor;
  		mReactantDescriptor = reactantDescriptor;
  		mProductDescriptor = productDescriptor;
  		mReactionCenterSimilarity = reactionCenterSimilarity;
  		mPeripherySimilarity = peripherySimilarity;
  		}
  
  	/**
  	 * Creates a complete specification for a reaction substructure search
  	 * with one or more query generic reactions.
  	 * @param searchType one of TYPE_...
  	 * @param query list of encoded query reactions
  	 * @param reactionDescriptor null or query reaction descriptors
  	 * @param reactantDescriptor null or reactant FFP512 descriptors
  	 * @param productDescriptor null or product FFP512 descriptors
  	 */
  	public ReactionSearchSpecification(int searchType, String[] query,
  	                                   long[][] reactionDescriptor, long[][] reactantDescriptor, long[][] productDescriptor) {
  		mSearchType = searchType;
  		mQuery = query;
  		mReactionDescriptor = reactionDescriptor;
  		mReactantDescriptor = reactantDescriptor;
  		mProductDescriptor = productDescriptor;
  	}
  
  	/**
  	 * Creates a complete specification for a retron search
  	 * with one or more query retron substructures.
  	 * @param query list of encoded retron structures
  	 * @param retronDescriptor null or product FFP512 descriptors
  	 */
  	public ReactionSearchSpecification(String[] query, long[][] retronDescriptor) {
  		mSearchType = TYPE_RETRON;
  		mQuery = query;
  		mRetronDescriptor = retronDescriptor;
  		}
  
  	/**
  	 * Returns the search type as integer including mode flags.
  	 * In case of TYPE_SIMILARITY use getDescriptorShortName() and
  	 * getSimilarityThreshold() for a full search specification.
  	 * @return one of TYPE_... and possibly MODE_LARGEST_FRAGMENT_ONLY
  	 *
  	public int getSearchType() {
  		return mSearchType;
  		}	*/
  
  	public int getReactionCount() {
  		return (mQuery == null) ? 0 : mQuery.length;
  		}
  
  	/**
  	 * Returns the (or one of the) query structures encodes as idcode.
  	 * @param index
  	 * @return
  	 */
  	public String getEncodedQuery(int index) {
  		return mQuery[index];
  		}
  
  	/**
  	 * @param index
  	 * @return
  	 */
  	public long[] getReactionDescriptor(int index) {
  		return (mReactionDescriptor == null) ? null : mReactionDescriptor[index];
  		}
  
  	/**
  	 * @param index
  	 * @return
  	 */
  	public long[] getReactantDescriptor(int index) {
  		return (mReactantDescriptor == null) ? null : mReactantDescriptor[index];
  		}
  
  	/**
  	 * @param index
  	 * @return
  	 */
  	public long[] getProductDescriptor(int index) {
  		return (mProductDescriptor == null) ? null : mProductDescriptor[index];
  		}
  
  	/**
  	 * @param index
  	 * @return
  	 */
  	public long[] getRetronDescriptor(int index) {
  		return (mReactionDescriptor == null) ? null : mReactionDescriptor[index];
  		}
  
  	public boolean isSimilaritySearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_SIMILARITY;
  		}
  
  	/**
  	 * @return whether this search does not include a structure search component is uses exclusively external criteria
  	 */
  	public boolean isNoReactionSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_NO_REACTION;
  		}
  
  	public boolean isSubreactionSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_SUBREACTION;
  		}
  
  	public boolean isRetronSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_RETRON;
  	}
  
  	/**
  	 * An exact search is a comparison of idcodes of
  	 * standardized molecules with full stereo features.
  	 * @return
  	 */
  	public boolean isExactSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_EXACT_STRICT;
  		}
  
  	/**
  	 * A noStereo search is a hash code comparison from
  	 * encoding stereo depleted structures.
  	 * @return
  	 */
  	public boolean isNoStereoSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_EXACT_NO_STEREO;
  		}
  
  	public void removeDescriptors() {
  		mReactionDescriptor = null;
  		mReactantDescriptor = null;
  		mProductDescriptor = null;
  		mRetronDescriptor = null;
  		}
  
  	public float getReactionCenterSimilarity() {
  		return mReactionCenterSimilarity;
  		}
  
  	public float getPeripherySimilarity() {
  		return mPeripherySimilarity;
  		}
  
  	/**
  	 * Checks, whether this specification is correctly defining a search.
  	 * If something is missing or inconsistent, an error message
  	 * describing the problem is returned.
  	 * @return null or error message
  	 */
  	public String validate() {
  		int count = getReactionCount();
  		if (count == 0)
  			return "No query reactions defined.";
  
  		for (int i=0; i<count; i++) {
  			if (getEncodedQuery(i) == null || getEncodedQuery(i).length() == 0)   // TODO better validity checking
  				return "Empty reaction among query reactions.";
  			}
  
  		if (isSimilaritySearch()) {
  			if (getReactionCenterSimilarity() < 0.5 || getReactionCenterSimilarity() > 1.0)
  				return "Reaction center similarity threshold out of allowed range.";
  			if (getPeripherySimilarity() < 0.0 || getPeripherySimilarity() > 1.0)
  				return "Periphery similarity threshold out of allowed range.";
  			}
  
  		return null;
  		}
  
  	@Override
  	public String toString() {
  		int type = mSearchType & TYPE_MASK;
  		String typeString = ((type == TYPE_SUBREACTION) 	? "subreaction"
  						   : (type == TYPE_SIMILARITY)		? "similarity("+mReactionCenterSimilarity+"/"+mPeripherySimilarity+")"
  						   : (type == TYPE_RETRON)      	? "retron"
  						   : (type == TYPE_EXACT_STRICT)	? "exact"
  						   : (type == TYPE_EXACT_NO_STEREO)	? "noStereo" : "undefined");
  
  		return "type:"+typeString
  			 + (mQuery==null?" reaction:null": mQuery.length==1?" reaction:"+(mQuery[0]==null?"null": mQuery[0]):" reactionCount:"+ mQuery.length)
  			 + (mReactionDescriptor==null?"":" reactionDescriptorCount:"+mReactionDescriptor.length)
  			 + (mReactantDescriptor==null?"":" reactantDescriptorCount:"+mReactantDescriptor.length)
  			 + (mProductDescriptor==null?"":" productDescriptorCount:"+mProductDescriptor.length)
  			 + (mRetronDescriptor==null?"":" retronDescriptorCount:"+mRetronDescriptor.length);
  		}
  	}
  