Class | Line # | Actions | ||||
---|---|---|---|---|---|---|
ColourSchemeI | 30 | 0 | 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.schemes; | |
22 | ||
23 | import jalview.datamodel.AnnotatedCollectionI; | |
24 | import jalview.datamodel.SequenceCollectionI; | |
25 | import jalview.datamodel.SequenceI; | |
26 | ||
27 | import java.awt.Color; | |
28 | import java.util.Map; | |
29 | ||
30 | public interface ColourSchemeI | |
31 | { | |
32 | /** | |
33 | * Returns the possibly context dependent colour for the given symbol at the | |
34 | * aligned position in the given sequence. For example, the colour may depend | |
35 | * on the symbol's relationship to the consensus residue for the column. | |
36 | * | |
37 | * @param symbol | |
38 | * @param position | |
39 | * @param seq | |
40 | * @param consensusResidue | |
41 | * the modal symbol (e.g. K) or symbols (e.g. KF) for the column | |
42 | * @param pid | |
43 | * the percentage identity of the column's consensus (if known) | |
44 | * @return | |
45 | */ | |
46 | Color findColour(char symbol, int position, SequenceI seq, | |
47 | String consensusResidue, float pid); | |
48 | ||
49 | /** | |
50 | * Recalculate dependent data using the given sequence collection, taking | |
51 | * account of hidden rows | |
52 | * | |
53 | * @param alignment | |
54 | * @param hiddenReps | |
55 | */ | |
56 | void alignmentChanged(AnnotatedCollectionI alignment, | |
57 | Map<SequenceI, SequenceCollectionI> hiddenReps); | |
58 | ||
59 | /** | |
60 | * Creates and returns a new instance of the colourscheme configured to colour | |
61 | * the given collection. Note that even simple colour schemes should return a | |
62 | * new instance for each call to this method, as different instances may have | |
63 | * differing shading by consensus or percentage identity applied. | |
64 | * | |
65 | * @param sg | |
66 | * @param hiddenRepSequences | |
67 | * @return copy of current scheme with any inherited settings transferred | |
68 | */ | |
69 | ColourSchemeI getInstance(AnnotatedCollectionI sg, | |
70 | Map<SequenceI, SequenceCollectionI> hiddenRepSequences); | |
71 | ||
72 | /** | |
73 | * Answers true if the colour scheme is suitable for the given data, else | |
74 | * false. For example, some colour schemes are specific to either peptide or | |
75 | * nucleotide, or only apply if certain kinds of annotation are present. | |
76 | * | |
77 | * @param ac | |
78 | * @return | |
79 | */ | |
80 | // TODO can make this method static in Java 8 | |
81 | boolean isApplicableTo(AnnotatedCollectionI ac); | |
82 | ||
83 | /** | |
84 | * Answers the 'official' name of the colour scheme (as used, for example, as | |
85 | * a Jalview startup parameter) | |
86 | * | |
87 | * @return | |
88 | */ | |
89 | String getSchemeName(); | |
90 | ||
91 | /** | |
92 | * Answers true if the colour scheme depends only on the sequence symbol, and | |
93 | * not on other information such as alignment consensus or annotation. (Note | |
94 | * that simple colour schemes may have a fading by percentage identity or | |
95 | * conservation overlaid.) Simple colour schemes can be propagated to | |
96 | * structure viewers. | |
97 | * | |
98 | * @return | |
99 | */ | |
100 | boolean isSimple(); | |
101 | ||
102 | /** | |
103 | * Answers true if the colour scheme has a colour specified for gaps. | |
104 | * | |
105 | * @return | |
106 | */ | |
107 | boolean hasGapColour(); | |
108 | } |