Class |
Line # |
Actions |
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AnnotationWorker | 37 | 35 | 12 |
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.workers; | |
22 | ||
23 | import jalview.api.AlignViewportI; | |
24 | import jalview.api.AlignmentViewPanel; | |
25 | import jalview.datamodel.AlignmentAnnotation; | |
26 | import jalview.datamodel.AlignmentI; | |
27 | import jalview.renderer.seqfeatures.FeatureRenderer; | |
28 | ||
29 | import java.util.ArrayList; | |
30 | import java.util.List; | |
31 | ||
32 | /** | |
33 | * A class to create and update one or more alignment annotations, given a | |
34 | * 'calculator'. Intended to support a 'plug-in' annotation worker which | |
35 | * implements the AnnotationProviderI interface. | |
36 | */ | |
37 | class AnnotationWorker extends AlignCalcWorker | |
38 | { | |
39 | /* | |
40 | * the provider of the annotation calculations | |
41 | */ | |
42 | AnnotationProviderI counter; | |
43 | ||
44 | /** | |
45 | * Constructor | |
46 | * | |
47 | * @param af | |
48 | * @param counter | |
49 | */ | |
50 | 2 | public AnnotationWorker(AlignViewportI viewport, AlignmentViewPanel panel, |
51 | AnnotationProviderI counter) | |
52 | { | |
53 | 2 | super(viewport, panel); |
54 | 2 | ourAnnots = new ArrayList<>(); |
55 | 2 | this.counter = counter; |
56 | 2 | calcMan.registerWorker(this); |
57 | } | |
58 | ||
59 | 2 | @Override |
60 | public void run() | |
61 | { | |
62 | 2 | try |
63 | { | |
64 | 2 | calcMan.notifyStart(this); |
65 | ||
66 | 2 | while (!calcMan.notifyWorking(this)) |
67 | { | |
68 | 0 | try |
69 | { | |
70 | 0 | Thread.sleep(200); |
71 | } catch (InterruptedException ex) | |
72 | { | |
73 | 0 | ex.printStackTrace(); |
74 | } | |
75 | } | |
76 | 2 | if (alignViewport.isClosed()) |
77 | { | |
78 | 0 | abortAndDestroy(); |
79 | 0 | return; |
80 | } | |
81 | ||
82 | // removeAnnotation(); | |
83 | 2 | AlignmentI alignment = alignViewport.getAlignment(); |
84 | 2 | if (alignment != null) |
85 | { | |
86 | 2 | try |
87 | { | |
88 | 2 | List<AlignmentAnnotation> anns = counter.calculateAnnotation( |
89 | alignment, new FeatureRenderer(alignViewport)); | |
90 | 2 | for (AlignmentAnnotation ann : anns) |
91 | { | |
92 | 2 | AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation( |
93 | ann.label, ann.description, false, null, null); | |
94 | 2 | theAnn.showAllColLabels = true; |
95 | 2 | theAnn.graph = AlignmentAnnotation.BAR_GRAPH; |
96 | 2 | theAnn.scaleColLabel = true; |
97 | 2 | theAnn.annotations = ann.annotations; |
98 | 2 | setGraphMinMax(theAnn, theAnn.annotations); |
99 | 2 | theAnn.validateRangeAndDisplay(); |
100 | 2 | if (!ourAnnots.contains(theAnn)) |
101 | { | |
102 | 1 | ourAnnots.add(theAnn); |
103 | } | |
104 | // alignment.addAnnotation(ann); | |
105 | } | |
106 | } catch (IndexOutOfBoundsException x) | |
107 | { | |
108 | // probable race condition. just finish and return without any fuss. | |
109 | 0 | return; |
110 | } | |
111 | } | |
112 | } catch (OutOfMemoryError error) | |
113 | { | |
114 | 0 | ap.raiseOOMWarning("calculating annotations", error); |
115 | 0 | calcMan.disableWorker(this); |
116 | } finally | |
117 | { | |
118 | 2 | calcMan.workerComplete(this); |
119 | } | |
120 | ||
121 | 2 | if (ap != null) |
122 | { | |
123 | 2 | ap.adjustAnnotationHeight(); |
124 | // TODO: only need to update colour and geometry if panel height changes | |
125 | // and view is coloured by annotation, and the annotation is actually | |
126 | // changed! | |
127 | 2 | ap.paintAlignment(true, true); |
128 | } | |
129 | } | |
130 | ||
131 | 0 | @Override |
132 | public void updateAnnotation() | |
133 | { | |
134 | // do nothing | |
135 | } | |
136 | ||
137 | /** | |
138 | * Answers true to indicate that if this worker's annotation is deleted from | |
139 | * the display, the worker should also be removed. This prevents it running | |
140 | * and recreating the annotation when the alignment changes. | |
141 | */ | |
142 | 0 | @Override |
143 | public boolean isDeletable() | |
144 | { | |
145 | 0 | return true; |
146 | } | |
147 | } |