JAL-2490 test coverage for printGffFormat before refactoring
[jalview.git] / test / jalview / ext / ensembl / EnsemblProteinTest.java
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 
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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.ensembl;
22
23 import static org.testng.AssertJUnit.assertEquals;
24
25 import jalview.gui.JvOptionPane;
26
27 import org.testng.Assert;
28 import org.testng.annotations.BeforeClass;
29 import org.testng.annotations.Test;
30
31 public class EnsemblProteinTest
32 {
33
34   @BeforeClass(alwaysRun = true)
35   public void setUpJvOptionPane()
36   {
37     JvOptionPane.setInteractiveMode(false);
38     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
39   }
40
41   @Test(groups = "Functional")
42   public void testIsValidReference() throws Exception
43   {
44     EnsemblSequenceFetcher esq = new EnsemblProtein();
45     Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
46     Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
47     Assert.assertFalse(esq.isValidReference("ENST00000288602"));
48     Assert.assertFalse(esq.isValidReference("ENSG00000288602"));
49     // non-human species having a 3 character identifier included:
50     Assert.assertTrue(esq.isValidReference("ENSMUSP00000099398"));
51   }
52
53   @Test(groups = "Functional")
54   public void testGetAccesionIdFromQuery() throws Exception
55   {
56     EnsemblSequenceFetcher esq = new EnsemblProtein();
57     assertEquals("ENSP00000288602",
58             esq.getAccessionIdFromQuery("ENSP00000288602"));
59     assertEquals("ENSMUSP00000288602",
60             esq.getAccessionIdFromQuery("ENSMUSP00000288602"));
61
62     // ENST converted to ENSP
63     assertEquals("ENSP00000288602",
64             esq.getAccessionIdFromQuery("ENST00000288602"));
65     assertEquals("ENSMUSP00000288602",
66             esq.getAccessionIdFromQuery("ENSMUST00000288602"));
67
68     // with valid separator:
69     assertEquals("ENSP00000288604",
70             esq.getAccessionIdFromQuery("ENSP00000288604 ENSP00000288602"));
71
72     // with wrong separator:
73     assertEquals("ENSP00000288604,ENSP00000288602",
74             esq.getAccessionIdFromQuery("ENSP00000288604,ENSP00000288602"));
75   }
76
77 }