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AlignViewControllerI | 40 | 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.api; | |
22 | ||
23 | import java.util.List; | |
24 | ||
25 | import jalview.io.DataSourceType; | |
26 | ||
27 | /** | |
28 | * prototype abstract controller for a Jalview alignment view | |
29 | * | |
30 | * @author jimp | |
31 | * | |
32 | * All operations should return true if the view has changed as a result | |
33 | * of the operation | |
34 | * | |
35 | * The controller holds methods that operate on an alignment view, | |
36 | * modifying its state in some way that may result in side effects | |
37 | * reflected in an associated GUI | |
38 | * | |
39 | */ | |
40 | public interface AlignViewControllerI | |
41 | { | |
42 | ||
43 | public boolean makeGroupsFromSelection(); | |
44 | ||
45 | public boolean createGroup(); | |
46 | ||
47 | public boolean unGroup(); | |
48 | ||
49 | public boolean deleteGroups(); | |
50 | ||
51 | public void setViewportAndAlignmentPanel(AlignViewportI viewport, | |
52 | AlignmentViewPanel alignPanel); | |
53 | ||
54 | /** | |
55 | * Mark columns in the current column selection according to positions of | |
56 | * sequence features | |
57 | * | |
58 | * @param invert | |
59 | * - when set, mark all but columns containing given type | |
60 | * @param extendCurrent | |
61 | * - when set, do not clear existing column selection | |
62 | * @param toggle | |
63 | * - rather than explicitly set, toggle selection state | |
64 | * @param featureType | |
65 | * - feature type string | |
66 | * @return true if operation affected state | |
67 | */ | |
68 | boolean markColumnsContainingFeatures(boolean invert, | |
69 | boolean extendCurrent, boolean toggle, String featureType); | |
70 | ||
71 | /** | |
72 | * sort the alignment or current selection by average score over the given set | |
73 | * of features | |
74 | * | |
75 | * @param typ | |
76 | * list of feature names or null to use currently displayed features | |
77 | */ | |
78 | void sortAlignmentByFeatureScore(List<String> typ); | |
79 | ||
80 | /** | |
81 | * sort the alignment or current selection by distribution of the given set of | |
82 | * features | |
83 | * | |
84 | * @param typ | |
85 | * list of feature names or null to use currently displayed features | |
86 | */ | |
87 | void sortAlignmentByFeatureDensity(List<String> typ); | |
88 | ||
89 | /** | |
90 | * add a features file of some kind to the current view | |
91 | * | |
92 | * @param file | |
93 | * @param sourceType | |
94 | * @param relaxedIdMatching | |
95 | * if true, try harder to match up IDs with local sequence data | |
96 | * @return true if parsing resulted in something being imported to the view or | |
97 | * dataset | |
98 | */ | |
99 | public boolean parseFeaturesFile(Object file, DataSourceType sourceType, | |
100 | boolean relaxedIdMatching); | |
101 | ||
102 | /** | |
103 | * mark columns containing highlighted regions (e.g. from search, structure | |
104 | * highlight, or a mouse over event in another viewer) | |
105 | * | |
106 | * @param invert | |
107 | * @param extendCurrent | |
108 | * @param toggle | |
109 | * @return | |
110 | */ | |
111 | boolean markHighlightedColumns(boolean invert, boolean extendCurrent, | |
112 | boolean toggle); | |
113 | ||
114 | /** | |
115 | * copies each distinct highlighted region on the current view as a new | |
116 | * sequence on the clipboard | |
117 | * | |
118 | * @return | |
119 | */ | |
120 | boolean copyHighlightedRegionsToClipboard(); | |
121 | ||
122 | /** | |
123 | * Justify alignment or currently selected region left or right | |
124 | * | |
125 | * @param left | |
126 | * - true - means justify left | |
127 | * @return | |
128 | */ | |
129 | boolean justify_Region(boolean left); | |
130 | } |