2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.datamodel;
20 import java.util.List;
23 public interface SequenceCollectionI
25 List<SequenceI> getSequences();
27 List<SequenceI> getSequences(
28 Map<SequenceI, SequenceCollectionI> hiddenReps);
32 * @return true if getSeqrep doesn't return null
36 * get the reference or representative sequence within this collection
37 * @return null or the current reference sequence
39 SequenceI getSeqrep();
41 * set the reference or representative sequence for this collection.
42 * Reference is assumed to be present within the collection.
45 void setSeqrep(SequenceI refseq);