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ClustalFileTest | 32 | 18 | 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; | |
22 | ||
23 | import static org.testng.Assert.assertEquals; | |
24 | import static org.testng.Assert.assertTrue; | |
25 | ||
26 | import jalview.datamodel.SequenceI; | |
27 | ||
28 | import java.io.IOException; | |
29 | ||
30 | import org.testng.annotations.Test; | |
31 | ||
32 | public class ClustalFileTest | |
33 | { | |
34 | 1 | @Test(groups = "Functional") |
35 | public void testParse_withNumbering() throws IOException | |
36 | { | |
37 | //@formatter:off | |
38 | 1 | String data = "CLUSTAL\n\n" |
39 | + "FER_CAPAA/1-8 -----------------------------------------------------------A\t1\n" | |
40 | + "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48\n" | |
41 | + "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n" | |
42 | + "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n" | |
43 | + "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53\n\n" | |
44 | + "FER_CAPAA/1-8 SYKVKLI 8\n" | |
45 | + "FER_CAPAN/1-55 SYKVKLI 55\n" | |
46 | + "FER1_SOLLC/1-55 SYKVKLI 55\n" | |
47 | + "Q93XJ9_SOLTU/1-55 SYKVKLI 55\n" | |
48 | + "FER1_PEA/1-60 SYKVKLV 60\n" | |
49 | + " .* .:....*******..** ..........** ********...*:::* ...\n" | |
50 | + "\t\t.:.::. *\n"; | |
51 | //@formatter:on | |
52 | 1 | ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE); |
53 | 1 | cf.parse(); |
54 | 1 | SequenceI[] seqs = cf.getSeqsAsArray(); |
55 | 1 | assertEquals(seqs.length, 5); |
56 | 1 | assertEquals(seqs[0].getName(), "FER_CAPAA"); |
57 | 1 | assertEquals(seqs[0].getStart(), 1); |
58 | 1 | assertEquals(seqs[0].getEnd(), 8); |
59 | 1 | assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI")); |
60 | } | |
61 | ||
62 | 1 | @Test(groups = "Functional") |
63 | public void testParse_noNumbering() throws IOException | |
64 | { | |
65 | //@formatter:off | |
66 | 1 | String data = "CLUSTAL\n\n" |
67 | + "FER_CAPAA/1-8 -----------------------------------------------------------A\n" | |
68 | + "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n" | |
69 | + "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n" | |
70 | + "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n" | |
71 | + "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n" | |
72 | + "FER_CAPAA/1-8 SYKVKLI\n" | |
73 | + "FER_CAPAN/1-55 SYKVKLI\n" | |
74 | + "FER1_SOLLC/1-55 SYKVKLI\n" | |
75 | + "Q93XJ9_SOLTU/1-55 SYKVKLI\n" | |
76 | + "FER1_PEA/1-60 SYKVKLV\n"; | |
77 | //@formatter:on | |
78 | 1 | ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE); |
79 | 1 | cf.parse(); |
80 | 1 | SequenceI[] seqs = cf.getSeqsAsArray(); |
81 | 1 | assertEquals(seqs.length, 5); |
82 | 1 | assertEquals(seqs[0].getName(), "FER_CAPAA"); |
83 | 1 | assertEquals(seqs[0].getStart(), 1); |
84 | 1 | assertEquals(seqs[0].getEnd(), 8); |
85 | 1 | assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI")); |
86 | } | |
87 | } |