forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java

   1 // $Id:
   2 // $
   3 //
   4 // FORESTER -- software libraries and applications
   5 // for evolutionary biology research and applications.
   6 //
   7 // Copyright (C) 2008-2009 Christian M. Zmasek
   8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   9 // All rights reserved
  10 //
  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.
  15 //
  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.
  20 //
  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
  24 //
  25 // Contact: phylosoft @ gmail . com
  26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  27
  28 package org.forester.surfacing;
  29
  30 import java.util.List;
  31 import java.util.SortedSet;
  32
  33 public interface DomainSimilarityCalculator {
  34
  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 );;
  39
  40                                                               public static enum Detailedness {
  41                                                                   BASIC, LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, PUNCTILIOUS
  42                                                               }
  43
  44                                                               public static enum GoAnnotationOutput {
  45                                                                   ALL, NONE
  46                                                               }
  47 }