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}