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GeneLociI | 28 | 0 | 0 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.datamodel; | |
22 | ||
23 | import jalview.util.MapList; | |
24 | ||
25 | /** | |
26 | * An interface to model one or more contiguous regions on one chromosome | |
27 | */ | |
28 | public interface GeneLociI | |
29 | { | |
30 | /** | |
31 | * Answers the species identifier | |
32 | * | |
33 | * @return | |
34 | */ | |
35 | String getSpeciesId(); | |
36 | ||
37 | /** | |
38 | * Answers the reference assembly identifier | |
39 | * | |
40 | * @return | |
41 | */ | |
42 | String getAssemblyId(); | |
43 | ||
44 | /** | |
45 | * Answers the chromosome identifier e.g. "2", "Y", "II" | |
46 | * | |
47 | * @return | |
48 | */ | |
49 | String getChromosomeId(); | |
50 | ||
51 | /** | |
52 | * Answers the mapping from sequence to chromosome loci. For a reverse strand | |
53 | * mapping, the chromosomal ranges will have start > end. | |
54 | * | |
55 | * @return | |
56 | */ | |
57 | MapList getMapping(); | |
58 | } |