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Jalview2xmlBase | 36 | 17 | 11 |
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.io; | |
22 | ||
23 | import java.util.Date; | |
24 | ||
25 | import org.testng.annotations.AfterClass; | |
26 | import org.testng.annotations.BeforeClass; | |
27 | import org.testng.annotations.BeforeTest; | |
28 | ||
29 | import jalview.bin.Cache; | |
30 | import jalview.bin.Jalview; | |
31 | import jalview.datamodel.AlignmentAnnotation; | |
32 | import jalview.datamodel.SequenceI; | |
33 | import jalview.gui.Desktop; | |
34 | import jalview.gui.JvOptionPane; | |
35 | ||
36 | public class Jalview2xmlBase | |
37 | { | |
38 | ||
39 | 0 | @BeforeClass(alwaysRun = true) |
40 | public void setUpJvOptionPane() | |
41 | { | |
42 | 0 | JvOptionPane.setInteractiveMode(false); |
43 | 0 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
44 | } | |
45 | ||
46 | /** | |
47 | * @throws java.lang.Exception | |
48 | */ | |
49 | 3 | @BeforeClass(alwaysRun = true) |
50 | public static void setUpBeforeClass() throws Exception | |
51 | { | |
52 | /* | |
53 | * use read-only test properties file | |
54 | */ | |
55 | 3 | Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
56 | ||
57 | /* | |
58 | * set news feed last read to a future time to ensure no | |
59 | * 'unread' news item is displayed | |
60 | */ | |
61 | 3 | Date oneHourFromNow = new Date( |
62 | System.currentTimeMillis() + 3600 * 1000); | |
63 | 3 | Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow); |
64 | ||
65 | 3 | Jalview.main(new String[] {}); |
66 | } | |
67 | ||
68 | /** | |
69 | * @throws java.lang.Exception | |
70 | */ | |
71 | 3 | @AfterClass(alwaysRun = true) |
72 | public static void tearDownAfterClass() throws Exception | |
73 | { | |
74 | 3 | if (Desktop.instance != null) |
75 | 3 | Desktop.instance.closeAll_actionPerformed(null); |
76 | } | |
77 | ||
78 | 4 | @BeforeTest(alwaysRun = true) |
79 | public static void clearDesktop() | |
80 | { | |
81 | 4 | if (Desktop.instance != null && Desktop.getFrames() != null |
82 | && Desktop.getFrames().length > 0) | |
83 | { | |
84 | 0 | Desktop.instance.closeAll_actionPerformed(null); |
85 | } | |
86 | } | |
87 | ||
88 | 2 | public int countDsAnn(jalview.viewmodel.AlignmentViewport avp) |
89 | { | |
90 | 2 | int numdsann = 0; |
91 | 2 | for (SequenceI sq : avp.getAlignment().getDataset().getSequences()) |
92 | { | |
93 | 122 | if (sq.getAnnotation() != null) |
94 | { | |
95 | 122 | for (AlignmentAnnotation dssa : sq.getAnnotation()) |
96 | { | |
97 | 122 | if (dssa.isValidStruc()) |
98 | { | |
99 | 122 | numdsann++; |
100 | } | |
101 | } | |
102 | } | |
103 | } | |
104 | 2 | return numdsann; |
105 | } | |
106 | ||
107 | } |