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SeqsetUtilsTest | 40 | 20 | 2 |
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.analysis; | |
22 | ||
23 | import jalview.datamodel.Alignment; | |
24 | import jalview.datamodel.AlignmentI; | |
25 | import jalview.datamodel.Sequence; | |
26 | import jalview.datamodel.SequenceFeature; | |
27 | import jalview.datamodel.SequenceI; | |
28 | import jalview.gui.JvOptionPane; | |
29 | ||
30 | import java.util.Hashtable; | |
31 | ||
32 | import org.testng.Assert; | |
33 | import org.testng.annotations.BeforeClass; | |
34 | import org.testng.annotations.Test; | |
35 | ||
36 | /** | |
37 | * @author jprocter | |
38 | * | |
39 | */ | |
40 | public class SeqsetUtilsTest | |
41 | { | |
42 | ||
43 | 1 | @BeforeClass(alwaysRun = true) |
44 | public void setUpJvOptionPane() | |
45 | { | |
46 | 1 | JvOptionPane.setInteractiveMode(false); |
47 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
48 | } | |
49 | ||
50 | /** | |
51 | * test for JAL-2046 bug - duplication of sequence features on reconstructed | |
52 | * alignment | |
53 | */ | |
54 | 1 | @Test(groups = { "Functional" }) |
55 | public void testSeqFeatureAddition() | |
56 | { | |
57 | 1 | SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"), |
58 | new Sequence("Aseq2", "AREALSEQ") }; | |
59 | ||
60 | 1 | AlignmentI al = new Alignment(sqset); |
61 | 1 | al.setDataset(null); |
62 | 1 | AlignmentI ds = al.getDataset(); |
63 | 1 | SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far"); |
64 | 1 | SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far"); |
65 | 1 | ds.getSequenceAt(0).addSequenceFeature(sf1); |
66 | 1 | Hashtable unq = SeqsetUtils.uniquify(sqset, true); |
67 | 1 | SequenceI[] sqset2 = new SequenceI[] { |
68 | new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()), | |
69 | new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) }; | |
70 | 1 | Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1); |
71 | 1 | Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty()); |
72 | 1 | ds.getSequenceAt(0).addSequenceFeature(sf2); |
73 | 1 | Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2); |
74 | 1 | SeqsetUtils.deuniquify(unq, sqset2); |
75 | // explicitly test that original sequence features still exist because they | |
76 | // are on the shared dataset sequence | |
77 | 1 | Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2); |
78 | 1 | Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2); |
79 | 1 | Assert.assertSame(sqset[0].getSequenceFeatures().get(0), |
80 | sqset2[0].getSequenceFeatures().get(0)); | |
81 | 1 | Assert.assertSame(sqset[0].getSequenceFeatures().get(1), |
82 | sqset2[0].getSequenceFeatures().get(1)); | |
83 | } | |
84 | } |