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SequenceOntologyTest | 32 | 53 | 6 |
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.ext.so; | |
22 | ||
23 | import static org.testng.AssertJUnit.assertFalse; | |
24 | import static org.testng.AssertJUnit.assertTrue; | |
25 | ||
26 | import jalview.gui.JvOptionPane; | |
27 | import jalview.io.gff.SequenceOntologyI; | |
28 | ||
29 | import org.testng.annotations.BeforeClass; | |
30 | import org.testng.annotations.Test; | |
31 | ||
32 | public class SequenceOntologyTest | |
33 | { | |
34 | ||
35 | 1 | @BeforeClass(alwaysRun = true) |
36 | public void setUpJvOptionPane() | |
37 | { | |
38 | 1 | JvOptionPane.setInteractiveMode(false); |
39 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
40 | } | |
41 | ||
42 | private SequenceOntologyI so; | |
43 | ||
44 | 1 | @BeforeClass(alwaysRun = true) |
45 | public void setUp() | |
46 | { | |
47 | 1 | long now = System.currentTimeMillis(); |
48 | 1 | try |
49 | { | |
50 | 1 | so = new SequenceOntology(); |
51 | } catch (Throwable t) | |
52 | { | |
53 | 0 | System.out.println("SOTest error "); |
54 | 0 | t.printStackTrace(System.err); |
55 | } | |
56 | 1 | long elapsed = System.currentTimeMillis() - now; |
57 | 1 | System.out.println( |
58 | "Load and cache of Sequence Ontology took " + elapsed + "ms"); | |
59 | } | |
60 | ||
61 | 1 | @Test(groups = "Functional") |
62 | public void testIsA() | |
63 | { | |
64 | 1 | assertFalse(so.isA(null, null)); |
65 | 1 | assertFalse(so.isA(null, "SO:0000087")); |
66 | 1 | assertFalse(so.isA("SO:0000087", null)); |
67 | 1 | assertFalse(so.isA("complete", "garbage")); |
68 | ||
69 | 1 | assertTrue(so.isA("SO:0000087", "SO:0000704")); |
70 | 1 | assertFalse(so.isA("SO:0000704", "SO:0000087")); |
71 | 1 | assertTrue(so.isA("SO:0000736", "SO:0000735")); |
72 | ||
73 | // same thing: | |
74 | 1 | assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence")); |
75 | // direct parent: | |
76 | 1 | assertTrue(so.isA("micronuclear_sequence", "organelle_sequence")); |
77 | // grandparent: | |
78 | 1 | assertTrue(so.isA("micronuclear_sequence", "sequence_location")); |
79 | // great-grandparent: | |
80 | 1 | assertTrue(so.isA("micronuclear_sequence", "sequence_attribute")); |
81 | ||
82 | // same thing by name / description: | |
83 | 1 | assertTrue(so.isA("micronuclear_sequence", "SO:0000084")); |
84 | 1 | assertTrue(so.isA("SO:0000084", "micronuclear_sequence")); |
85 | 1 | assertTrue(so.isA("SO:0000084", "SO:0000084")); |
86 | ||
87 | // SO name to description: | |
88 | 1 | assertTrue(so.isA("SO:0000084", "organelle_sequence")); |
89 | 1 | assertTrue(so.isA("SO:0000084", "sequence_location")); |
90 | 1 | assertTrue(so.isA("SO:0000084", "sequence_attribute")); |
91 | ||
92 | // description to SO name: | |
93 | 1 | assertTrue(so.isA("micronuclear_sequence", "SO:0000736")); |
94 | 1 | assertTrue(so.isA("micronuclear_sequence", "SO:0000735")); |
95 | 1 | assertTrue(so.isA("micronuclear_sequence", "SO:0000400")); |
96 | } | |
97 | ||
98 | 1 | @Test(groups = "Functional") |
99 | public void testIsCDS() | |
100 | { | |
101 | 1 | assertTrue(so.isA("CDS", "CDS")); |
102 | 1 | assertTrue(so.isA("CDS_predicted", "CDS")); |
103 | 1 | assertTrue(so.isA("transposable_element_CDS", "CDS")); |
104 | 1 | assertTrue(so.isA("edited_CDS", "CDS")); |
105 | 1 | assertTrue(so.isA("CDS_independently_known", "CDS")); |
106 | 1 | assertTrue(so.isA("CDS_fragment", "CDS")); |
107 | 1 | assertFalse(so.isA("CDS_region", "CDS"));// part_of |
108 | 1 | assertFalse(so.isA("polypeptide", "CDS")); // derives_from |
109 | } | |
110 | ||
111 | 1 | @Test(groups = "Functional") |
112 | public void testIsSequenceVariant() | |
113 | { | |
114 | 1 | assertFalse(so.isA("CDS", "sequence_variant")); |
115 | 1 | assertTrue(so.isA("sequence_variant", "sequence_variant")); |
116 | ||
117 | /* | |
118 | * these should all be sub-types of sequence_variant | |
119 | */ | |
120 | 1 | assertTrue(so.isA("structural_variant", "sequence_variant")); |
121 | 1 | assertTrue(so.isA("feature_variant", "sequence_variant")); |
122 | 1 | assertTrue(so.isA("gene_variant", "sequence_variant")); |
123 | 1 | assertTrue(so.isA("transcript_variant", "sequence_variant")); |
124 | 1 | assertTrue(so.isA("NMD_transcript_variant", "sequence_variant")); |
125 | 1 | assertTrue(so.isA("missense_variant", "sequence_variant")); |
126 | 1 | assertTrue(so.isA("synonymous_variant", "sequence_variant")); |
127 | 1 | assertTrue(so.isA("frameshift_variant", "sequence_variant")); |
128 | 1 | assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant")); |
129 | 1 | assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant")); |
130 | 1 | assertTrue(so.isA("stop_gained", "sequence_variant")); |
131 | 1 | assertTrue(so.isA("stop_lost", "sequence_variant")); |
132 | 1 | assertTrue(so.isA("inframe_deletion", "sequence_variant")); |
133 | 1 | assertTrue(so.isA("inframe_insertion", "sequence_variant")); |
134 | } | |
135 | } |