2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.protein;
28 public interface BinaryDomainCombination extends Comparable<BinaryDomainCombination> {
30 public static final String SEPARATOR = "=";
32 public DomainId getId0();
34 public DomainId getId1();
36 public abstract StringBuffer toGraphDescribingLanguage( final OutputFormat format,
37 final String node_attribute,
38 String edge_attribute );
41 * This has to return a String representation
42 * in the following format:
45 * @return a String representation in the form id0 - id1
48 public String toString();
50 public static enum DomainCombinationType {
51 BASIC, DIRECTED, DIRECTED_ADJACTANT;
54 public static enum OutputFormat {