2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.datamodel;
21 import java.util.List;
24 public interface SequenceCollectionI
26 List<SequenceI> getSequences();
28 List<SequenceI> getSequences(
29 Map<SequenceI, SequenceCollectionI> hiddenReps);
33 * @return true if getSeqrep doesn't return null
37 * get the reference or representative sequence within this collection
38 * @return null or the current reference sequence
40 SequenceI getSeqrep();
42 * set the reference or representative sequence for this collection.
43 * Reference is assumed to be present within the collection.
46 void setSeqrep(SequenceI refseq);
49 * @return the first column included in this collection. Runs from 0<=i<N_cols
56 * @return the last column in this collection. Runs from 0<=i<N_cols