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SearchResultMatchI | 27 | 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 | /** | |
24 | * An interface that describes one matched region of an alignment, as one | |
25 | * contiguous portion of a single dataset sequence | |
26 | */ | |
27 | public interface SearchResultMatchI | |
28 | { | |
29 | /** | |
30 | * Returns the matched sequence | |
31 | * | |
32 | * @return | |
33 | */ | |
34 | SequenceI getSequence(); | |
35 | ||
36 | /** | |
37 | * Returns the start position of the match in the sequence (base 1) | |
38 | * | |
39 | * @return | |
40 | */ | |
41 | int getStart(); | |
42 | ||
43 | /** | |
44 | * Returns the end position of the match in the sequence (base 1) | |
45 | * | |
46 | * @return | |
47 | */ | |
48 | int getEnd(); | |
49 | ||
50 | /** | |
51 | * Answers true if this match is for the given sequence and includes (matches | |
52 | * or encloses) the given start-end range | |
53 | * | |
54 | * @param seq | |
55 | * @param start | |
56 | * @param end | |
57 | * @return | |
58 | */ | |
59 | boolean contains(SequenceI seq, int start, int end); | |
60 | ||
61 | /** | |
62 | * | |
63 | * @param seq | |
64 | * @param from | |
65 | * - first position to highlight | |
66 | * @param to | |
67 | * - last position to highlight (assumed higher than from) | |
68 | * @return true iff from-to intersects or marks positions either side of | |
69 | * start/end | |
70 | */ | |
71 | boolean adjacent(SequenceI seq, int from, int to); | |
72 | } |