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GffHelperFactoryTest | 32 | 30 | 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.io.gff; | |
22 | ||
23 | import static org.testng.AssertJUnit.assertNull; | |
24 | import static org.testng.AssertJUnit.assertSame; | |
25 | import static org.testng.AssertJUnit.assertTrue; | |
26 | ||
27 | import jalview.gui.JvOptionPane; | |
28 | ||
29 | import org.testng.annotations.BeforeClass; | |
30 | import org.testng.annotations.Test; | |
31 | ||
32 | public class GffHelperFactoryTest | |
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 | 1 | @Test(groups = "Functional") |
43 | public void testGetHelper() | |
44 | { | |
45 | 1 | assertNull(GffHelperFactory.getHelper(null)); |
46 | ||
47 | 1 | String tabRegex = "\\t"; |
48 | ||
49 | /* | |
50 | * column 3 = 'similarity' indicates exonerate GFF alignment data | |
51 | */ | |
52 | 1 | String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t"; |
53 | // no attributes (column 9 data): | |
54 | 1 | assertTrue(GffHelperFactory |
55 | .getHelper(gff.split(tabRegex)) instanceof Gff2Helper); | |
56 | ||
57 | // attributes set but unhandled featureGroup - get generic handler | |
58 | 1 | gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1"; |
59 | 1 | assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(), |
60 | Gff3Helper.class); | |
61 | ||
62 | // handled featureGroup (exonerate model) values | |
63 | 1 | gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1"; |
64 | 1 | assertTrue(GffHelperFactory |
65 | .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper); | |
66 | ||
67 | 1 | gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1"; |
68 | 1 | assertTrue(GffHelperFactory |
69 | .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper); | |
70 | ||
71 | 1 | gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1"; |
72 | 1 | assertTrue(GffHelperFactory |
73 | .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper); | |
74 | ||
75 | 1 | gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1"; |
76 | 1 | assertTrue(GffHelperFactory |
77 | .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper); | |
78 | ||
79 | 1 | gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1"; |
80 | 1 | assertTrue(GffHelperFactory |
81 | .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper); | |
82 | ||
83 | 1 | gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1"; |
84 | 1 | assertTrue(GffHelperFactory |
85 | .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper); | |
86 | ||
87 | // not case-sensitive: | |
88 | 1 | gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1"; |
89 | 1 | assertTrue(GffHelperFactory |
90 | .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper); | |
91 | ||
92 | /* | |
93 | * InterProScan has 'protein_match' in column 3 | |
94 | */ | |
95 | 1 | gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154"; |
96 | 1 | assertTrue(GffHelperFactory |
97 | .getHelper(gff.split(tabRegex)) instanceof InterProScanHelper); | |
98 | ||
99 | /* | |
100 | * nothing specific - return the generic GFF3 class if Name=Value is present in col9 | |
101 | */ | |
102 | 1 | gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1"; |
103 | 1 | GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex)); |
104 | 1 | assertSame(helper.getClass(), Gff3Helper.class); |
105 | ||
106 | // return the generic GFF2 class if "Name Value" is present in col9 | |
107 | 1 | gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1"; |
108 | 1 | helper = GffHelperFactory.getHelper(gff.split(tabRegex)); |
109 | 1 | assertSame(helper.getClass(), Gff2Helper.class); |
110 | } | |
111 | } |