2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ext.ensembl;
23 import static org.testng.AssertJUnit.assertEquals;
25 import org.testng.Assert;
26 import org.testng.annotations.Test;
28 public class EnsemblProteinTest
31 @Test(groups = "Functional")
32 public void testIsValidReference() throws Exception
34 EnsemblSequenceFetcher esq = new EnsemblProtein();
35 Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
36 Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
37 Assert.assertFalse(esq.isValidReference("ENST00000288602"));
38 Assert.assertFalse(esq.isValidReference("ENSG00000288602"));
39 // non-human species having a 3 character identifier included:
40 Assert.assertTrue(esq.isValidReference("ENSMUSP00000099398"));
43 @Test(groups = "Functional")
44 public void testGetAccesionIdFromQuery() throws Exception
46 EnsemblSequenceFetcher esq = new EnsemblProtein();
47 assertEquals("ENSP00000288602",
48 esq.getAccessionIdFromQuery("ENSP00000288602"));
49 assertEquals("ENSMUSP00000288602",
50 esq.getAccessionIdFromQuery("ENSMUSP00000288602"));
52 // ENST converted to ENSP
53 assertEquals("ENSP00000288602",
54 esq.getAccessionIdFromQuery("ENST00000288602"));
55 assertEquals("ENSMUSP00000288602",
56 esq.getAccessionIdFromQuery("ENSMUST00000288602"));
58 // with valid separator:
59 assertEquals("ENSP00000288604",
60 esq.getAccessionIdFromQuery("ENSP00000288604 ENSP00000288602"));
62 // with wrong separator:
63 assertEquals("ENSP00000288604,ENSP00000288602",
64 esq.getAccessionIdFromQuery("ENSP00000288604,ENSP00000288602"));