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.chem.descriptor.DescriptorHelper;
  
  import java.io.Serializable;
  import java.nio.charset.StandardCharsets;
  
  public class StructureSearchSpecification implements Serializable {
      static final long serialVersionUID = 0x20120402;
  
  	private static final int TYPE_MASK				= 0x0000FF;
  	public static final int TYPE_NO_STRUCTURE		= 0x000000; // no structure search (other criteria only)
  	public static final int TYPE_SUBSTRUCTURE		= 0x000001;
  	public static final int TYPE_SIMILARITY			= 0x000002;
  	public static final int TYPE_EXACT_STRICT		= 0x000003;
  	public static final int TYPE_EXACT_NO_STEREO	= 0x000004;
  	public static final int TYPE_TAUTOMER			= 0x000005;
  	public static final int TYPE_TAUTOMER_NO_STEREO	= 0x000006;
  	public static final int TYPE_BACKBONE_NO_STEREO	= 0x000007;
  
  	public static final int MODE_LARGEST_FRAGMENT_ONLY	= 0x000100;
  	public static final int MODE_SINGLE_MATCH_ONLY = 0x000200;
  
  	private int mSearchType;
  	private byte[][] mIDCode;
  	private Object[] mDescriptor;
  	private String mDescriptorShortName;
  	private float mSimilarityThreshold;
  
  	/**
  	 * Creates a complete specification for a substructure or similarity search
  	 * with one or more query fragments or molecules.
  	 * @param searchType one of TYPE_... + optionally MODE_...
  	 * @param idcode list of query fragments/molecules
  	 * @param descriptor null or list descriptors (in case of substructure search this should be the long FFP512)
  	 * @param descriptorShortName in case of TYPE_SIMILARITY
  	 * @param similarityThreshold in case of TYPE_SIMILARITY
  	 */
  	public StructureSearchSpecification(int searchType, byte[][] idcode, Object[] descriptor, String descriptorShortName, float similarityThreshold) {
  		mSearchType = searchType;
  		mIDCode = idcode;
  		mDescriptor = descriptor;
  		mDescriptorShortName = descriptorShortName;
  		mSimilarityThreshold = similarityThreshold;
  		}
  
  	/**
  	 * 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 getStructureCount() {
  		return (mIDCode == null) ? 0 : mIDCode.length;
  		}
  
  	/**
  	 * Returns the (or one of the) query structures encodes as idcode.
  	 * @param index
  	 * @return
  	 */
  	public byte[] getIDCode(int index) {
  		return mIDCode[index];
  		}
  
  	/**
  	 * Depending on the mode isLargestFragmentOnly() the descriptor
  	 * is expected to be represent the whole structure or the largest fragment.
  	 * @param index
  	 * @return
  	 */
  	public Object getDescriptor(int index) {
  		return (mDescriptor == null) ? null : mDescriptor[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 isNoStructureSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_NO_STRUCTURE;
  		}
  
  	public boolean isSubstructureSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_SUBSTRUCTURE;
  		}
  
  	/**
  	 * 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;
  		}
  
  	/**
  	 * A tautomer search is a hash code comparison from
  	 * encoding generic tautomer structures.
  	 * @return
  	 */
  	public boolean isTautomerSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_TAUTOMER;
  		}
  
  	/**
  	 * A no-stereo-tautomer search is a hash code comparison from
  	 * encoding stereo depleted generic tautomer structures.
  	 * @return
  	 */
  	public boolean isNoStereoTautomerSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_TAUTOMER_NO_STEREO;
  		}
  
  	/**
  	 * A backbone search is a hash code comparison from
  	 * encoding stereo and unsaturation depleted structures.
  	 * @return
  	 */
  	public boolean isBackboneSearch() {
  		return (mSearchType & TYPE_MASK) == TYPE_BACKBONE_NO_STEREO;
  		}
  
  	/**
  	 * This setting is relevant for all search types except the substructure search.
  	 * @return
  	 */
  	public boolean isLargestFragmentOnly() {
  		return (mSearchType & MODE_LARGEST_FRAGMENT_ONLY) != 0;
  		}
  
  	public boolean isSingleMatchOnly() {
  		return (mSearchType & MODE_SINGLE_MATCH_ONLY) != 0;
  	}
  
  	public void removeDescriptors() {
  		mDescriptor = null;
  		}
  
  	/**
  	 *
  	 * @param b
  	 */
  	public void setLargestFragmentOnly(boolean b) {
  		mSearchType &= ~MODE_LARGEST_FRAGMENT_ONLY;
  		if (b)
  			mSearchType |= MODE_LARGEST_FRAGMENT_ONLY;
  		}
  
  	/**
  	 * In case of a substructure search, as default a molecule is considered a match if the query
  	 * structure is found once or multiple times. To consider only single matches a match, call this
  	 * method with argument true.
  	 * @param b
  	 */
  	public void setSingleMatchOnly(boolean b) {
  		mSearchType &= ~MODE_SINGLE_MATCH_ONLY;
  		if (b)
  			mSearchType |= MODE_SINGLE_MATCH_ONLY;
  		}
  
  	public String getDescriptorShortName() {
  		return mDescriptorShortName;
  		}
  
  	public float getSimilarityThreshold() {
  		return mSimilarityThreshold;
  		}
  
  	/**
  	 * 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 = getStructureCount();
  		if (count == 0)
  			return "No query structures defined.";
  
  		for (int i=0; i<count; i++)
  			if (new IDCodeParser(false).getAtomCount(getIDCode(i), 0) == 0)
  				return "Empty structure among query structures.";
  
  		if (isSimilaritySearch()) {
  			if (!DescriptorHelper.isDescriptorShortName(getDescriptorShortName()))
  				return "No descriptor type defined.";
  			if (getSimilarityThreshold() < 0.5 || getSimilarityThreshold() > 1.0)
  				return "Similarity threshold out of allowed range.";
  			}
  
  		return null;
  		}
  
  	@Override
  	public String toString() {
  		int type = mSearchType & TYPE_MASK;
  		String typeString = ((type == TYPE_SUBSTRUCTURE)	? "substructure"
  						   : (type == TYPE_SIMILARITY)		? "similarity/"+mDescriptorShortName+"("+mSimilarityThreshold+")"
  						   : (type == TYPE_EXACT_STRICT)	? "exact"
  						   : (type == TYPE_EXACT_NO_STEREO)	? "noStereo"
  						   : (type == TYPE_TAUTOMER)		? "tautomer"
  						   : (type == TYPE_TAUTOMER_NO_STEREO)	? "no-stereo tautomer"
  						   : (type == TYPE_BACKBONE_NO_STEREO)	? "backbone" : "undefined")
  						  + (((mSearchType & MODE_LARGEST_FRAGMENT_ONLY) != 0) ? "/largestFragmentOnly":"");
  
  		return "type:"+typeString
  			 + (mIDCode==null?" idcodes:null":mIDCode.length==1?" idcode:"+(mIDCode[0]==null?"null":new String(mIDCode[0], StandardCharsets.UTF_8)):" idcodeCount:"+mIDCode.length)
  			 + (mDescriptor==null?" descriptors:null":" descriptorCount:"+mDescriptor.length);
  		}
  	}
  