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 * Created on June 7, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment.template;
025
026import org.biojava.nbio.core.sequence.template.Compound;
027import org.biojava.nbio.core.sequence.template.Sequence;
028
029/**
030 * Defines a clustering algorithm that converts a distance matrix into a tree.
031 *
032 * @author Mark Chapman
033 * @param <S> each {@link Sequence} in the tree is of type S
034 * @param <C> each element of a {@link Sequence} is a {@link Compound} of type C
035 */
036public interface HierarchicalClusterer<S extends Sequence<C>, C extends Compound> {
037
038        /**
039         * Returns the distance matrix used in clustering.  May be calculated from another original source.
040         *
041         * @return the distance matrix input to clustering
042         */
043        float[][] getDistanceMatrix();
044
045        /**
046         * Returns the root node of the tree resulting from this clustering algorithm.
047         *
048         * @return the resulting tree output from clustering
049         */
050        GuideTreeNode<S, C> getRoot();
051
052}