Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
RNAMLfileTest | 39 | 8 | 5 |
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 jalview.datamodel.SequenceI; | |
24 | import jalview.gui.JvOptionPane; | |
25 | ||
26 | import static org.testng.Assert.assertEquals; | |
27 | import static org.testng.Assert.assertNotNull; | |
28 | ||
29 | import java.io.File; | |
30 | import java.io.IOException; | |
31 | ||
32 | import org.testng.annotations.AfterClass; | |
33 | import org.testng.annotations.BeforeClass; | |
34 | import org.testng.annotations.Test; | |
35 | ||
36 | import fr.orsay.lri.varna.utils.RNAMLParser; | |
37 | import groovy.lang.Sequence; | |
38 | ||
39 | public class RNAMLfileTest | |
40 | { | |
41 | ||
42 | 1 | @BeforeClass(alwaysRun = true) |
43 | public void setUpJvOptionPane() | |
44 | { | |
45 | 1 | JvOptionPane.setInteractiveMode(false); |
46 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
47 | } | |
48 | ||
49 | 1 | @BeforeClass(alwaysRun = true) |
50 | public static void setUpBeforeClass() throws Exception | |
51 | { | |
52 | } | |
53 | ||
54 | 1 | @AfterClass(alwaysRun = true) |
55 | public static void tearDownAfterClass() throws Exception | |
56 | { | |
57 | } | |
58 | ||
59 | 1 | @Test(groups = { "Functional" }) |
60 | public void testRnamlToStockholmIO() | |
61 | { | |
62 | 1 | StockholmFileTest.testFileIOwithFormat( |
63 | new File("examples/testdata/rna-alignment.xml"), | |
64 | FileFormat.Stockholm, -1, -1, true, true, true); | |
65 | ||
66 | } | |
67 | ||
68 | 1 | @Test(groups = { "Functional" }) |
69 | public void testRnamlSeqImport() throws IOException | |
70 | { | |
71 | 1 | RnamlFile parser = new RnamlFile("examples/testdata/7WKP-rna1.xml", |
72 | DataSourceType.FILE); | |
73 | 1 | SequenceI[] seqs = parser.getSeqsAsArray(); |
74 | 1 | assertNotNull(seqs); |
75 | 1 | assertEquals(seqs.length, 1); |
76 | 1 | assertEquals(seqs[0].getEnd() - seqs[0].getStart() + 1, |
77 | seqs[0].getSequence().length); | |
78 | } | |
79 | ||
80 | } |