4 // FORESTER -- software libraries and applications
5 // for evolutionary biology research and applications.
7 // Copyright (C) 2008-2009 Christian M. Zmasek
8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: www.phylosoft.org/forester
28 package org.forester.surfacing;
30 import java.util.List;
31 import java.util.SortedSet;
33 public interface DomainSimilarityCalculator {
35 public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
36 final List<GenomeWideCombinableDomains> cdc_list,
37 final boolean ignore_domains_without_combinations_in_any_genome,
38 final boolean ignore_domains_specific_to_one_genome );;
40 public static enum Detailedness {
41 BASIC, LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, PUNCTILIOUS
44 public static enum GoAnnotationOutput {