Class |
Line # |
Actions |
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ContactListProviderI | 25 | 2 | 2 |
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 java.awt.Color; | |
24 | ||
25 | public interface ContactListProviderI | |
26 | { | |
27 | ||
28 | /** | |
29 | * | |
30 | * @return position index for this contact List (usually sequence position or | |
31 | * alignment column) | |
32 | */ | |
33 | int getPosition(); | |
34 | ||
35 | /** | |
36 | * dimension of list where getContactAt(column<getContactHeight()) may return | |
37 | * a value | |
38 | * | |
39 | * @return | |
40 | */ | |
41 | int getContactHeight(); | |
42 | ||
43 | /** | |
44 | * get a value representing contact at column for this site | |
45 | * | |
46 | * @param column | |
47 | * @return Double.NaN or a contact strength for this site | |
48 | */ | |
49 | double getContactAt(int column); | |
50 | ||
51 | /** | |
52 | * Return positions in local reference corresponding to cStart and cEnd in | |
53 | * matrix data. Positions are base 1 column indices for sequence associated | |
54 | * matrices. | |
55 | * | |
56 | * @param cStart | |
57 | * @param cEnd | |
58 | * @return int[] { start, end (inclusive) for each contiguous segment} | |
59 | */ | |
60 | 0 | default int[] getMappedPositionsFor(int cStart, int cEnd) |
61 | { | |
62 | 0 | return new int[] { cStart, cEnd }; |
63 | } | |
64 | ||
65 | 0 | default Color getColourForGroup() |
66 | { | |
67 | 0 | return null; |
68 | } | |
69 | ||
70 | } |