001package com.hfg.bio.phylogeny; 002 003import com.hfg.bio.seq.BioSequence; 004 005 006//------------------------------------------------------------------------------ 007/** 008 Interface defining a distance matrix calculation method. 009 010 See the <a href='http://embossgui.sourceforge.net/demo/manual/distmat.html'>emboss distmat manual</a> 011 for simple descriptions of some of the common methods. 012 013 @author J. Alex Taylor, hairyfatguy.com 014 */ 015//------------------------------------------------------------------------------ 016// com.hfg Library 017// 018// This library is free software; you can redistribute it and/or 019// modify it under the terms of the GNU Lesser General Public 020// License as published by the Free Software Foundation; either 021// version 2.1 of the License, or (at your option) any later version. 022// 023// This library is distributed in the hope that it will be useful, 024// but WITHOUT ANY WARRANTY; without even the implied warranty of 025// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 026// Lesser General Public License for more details. 027// 028// You should have received a copy of the GNU Lesser General Public 029// License along with this library; if not, write to the Free Software 030// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 031// 032// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com 033// jataylor@hairyfatguy.com 034//------------------------------------------------------------------------------ 035 036public interface DistanceMatrixModel 037{ 038 public String name(); 039 040 public float calculateDistance(BioSequence inSeq1, BioSequence inSeq2); 041 042}