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Line # |
Actions |
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RNAHelicesColourChooser | 40 | 25 | 8 |
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.api.AlignViewportI; | |
24 | import jalview.api.AlignmentViewPanel; | |
25 | import jalview.datamodel.AlignmentAnnotation; | |
26 | import jalview.datamodel.SequenceGroup; | |
27 | ||
28 | import java.util.Hashtable; | |
29 | import java.util.Map; | |
30 | import java.util.Vector; | |
31 | ||
32 | /** | |
33 | * Helps generate the colors for RNA secondary structure. Future: add option to | |
34 | * change colors based on covariation. | |
35 | * | |
36 | * @author Lauren Michelle Lui | |
37 | * @deprecated this seems to be unfinished - just use RNAHelicesColour | |
38 | */ | |
39 | @Deprecated | |
40 | public class RNAHelicesColourChooser | |
41 | { | |
42 | ||
43 | AlignViewportI av; | |
44 | ||
45 | AlignmentViewPanel ap; | |
46 | ||
47 | ColourSchemeI oldcs; | |
48 | ||
49 | Map<SequenceGroup, ColourSchemeI> oldgroupColours; | |
50 | ||
51 | AlignmentAnnotation currentAnnotation; | |
52 | ||
53 | boolean adjusting = false; | |
54 | ||
55 | 0 | public RNAHelicesColourChooser(AlignViewportI av, |
56 | final AlignmentViewPanel ap) | |
57 | { | |
58 | 0 | oldcs = av.getGlobalColourScheme(); |
59 | 0 | if (av.getAlignment().getGroups() != null) |
60 | { | |
61 | 0 | oldgroupColours = new Hashtable<>(); |
62 | 0 | for (SequenceGroup sg : ap.getAlignment().getGroups()) |
63 | { | |
64 | 0 | if (sg.getColourScheme() != null) |
65 | { | |
66 | 0 | oldgroupColours.put(sg, sg.getColourScheme()); |
67 | } | |
68 | } | |
69 | } | |
70 | 0 | this.av = av; |
71 | 0 | this.ap = ap; |
72 | ||
73 | 0 | adjusting = true; |
74 | 0 | Vector<String> list = new Vector<>(); |
75 | 0 | int index = 1; |
76 | 0 | AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); |
77 | 0 | if (anns != null) |
78 | { | |
79 | 0 | for (int i = 0; i < anns.length; i++) |
80 | { | |
81 | 0 | String label = anns[i].label; |
82 | 0 | if (!list.contains(label)) |
83 | { | |
84 | 0 | list.addElement(label); |
85 | } | |
86 | else | |
87 | { | |
88 | 0 | list.addElement(label + "_" + (index++)); |
89 | } | |
90 | } | |
91 | } | |
92 | ||
93 | 0 | adjusting = false; |
94 | 0 | changeColour(); |
95 | } | |
96 | ||
97 | 0 | void changeColour() |
98 | { | |
99 | // Check if combobox is still adjusting | |
100 | 0 | if (adjusting) |
101 | { | |
102 | 0 | return; |
103 | } | |
104 | 0 | RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment()); |
105 | ||
106 | 0 | av.setGlobalColourScheme(rhc); |
107 | ||
108 | 0 | ap.paintAlignment(true, true); |
109 | } | |
110 | } |