001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021
022package org.biojava.bio.search;
023
024import java.util.List;
025import java.util.Map;
026
027import org.biojava.bio.Annotatable;
028import org.biojava.bio.seq.Sequence;
029import org.biojava.bio.seq.db.SequenceDB;
030
031/**
032 * Objects of this type represent one particular result of a sequence
033 * similarity search.
034 *
035 * @author Gerald Loeffler
036 * @author Keith James
037 */
038public interface SeqSimilaritySearchResult extends Annotatable
039{
040    /**
041     * Returns the query sequence which was used to perform the search.
042     *
043     * @return the <code>Sequence</code> object used to search the
044     * <code>SequenceDB</code>. Never returns null.
045     */
046    public Sequence getQuerySequence();
047
048    /**
049     * Returns the sequence database against which the search was
050     * performed.
051     *
052     * @return the <code>SequenceDB object</code> against which the
053     * search was carried out. Never returns null.
054     */
055    public SequenceDB getSequenceDB();
056
057    /**
058     * Returns the search parameters used in the search that produced
059     * this search result.
060     *
061     * @return the (immutable) search parameter <code>Map
062     * object</code>. May return null.
063     */
064    public Map getSearchParameters();
065
066    /**
067     * Return all hits in this sequence similarity search result. The
068     * hits are sorted from best to worst.
069     *
070     * @return an (immutable) <code>List</code> of
071     * <code>SeqSimilaritySearchHit</code> objects containing all hits
072     * in the search result. Never returns null but may return an
073     * empty list.
074     */
075    public List getHits();
076}