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 */
021package org.biojava.bio.seq.homol;
022 
023import org.biojava.bio.alignment.Alignment;
024import org.biojava.bio.seq.FeatureHolder;
025import org.biojava.utils.ChangeType;
026
027/**
028 * <p>
029 * Signifies that two or more features are homologous.
030 * </p> 
031 *
032 * <p> Blast hits or local multiple-sequence alignments can be
033 * represented as a set of features on sequences that have an
034 * alignment. The features will probably implement
035 * HomologyFeature.
036 * </p>
037 *
038 * @author Matthew Pocock
039 * @author <a href="mailto:kdj@sanger.ac.uk">Keith James</a>
040 * @since 1.2
041 */
042public interface Homology {
043  /**
044   * Signals that the alignment describing the homologous sequences
045   * has changed. For implementations which implement
046   * <code>Changeable</code>.
047   */
048  public static final ChangeType ALIGNMENT =
049      new ChangeType("The alignment has been changed",
050                     "org.biojava.bio.seq.homol.Homology",
051                     "ALIGNMENT");
052
053  /**
054   * Retrieve the set of features that mark homologous regions.
055   *
056   * @return the FeatureHolder containing each homologous region
057   */
058  FeatureHolder getFeatures();
059  /**
060   * Retrieve the Alignment that specifies how the homologous regions are
061   * aligned. The labels of the alignment are the HomologyFeature objects.
062   *
063   * @return the Alignment between the HomologyFeatures
064   */
065  Alignment getAlignment();
066}