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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.ext.ensembl

File EnsemblProteinTest.java

 

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Classes

Class Line # Actions
EnsemblProteinTest 31 15 3 0
1.0100%
 

Contributing tests

This file is covered by 2 tests. .

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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.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  1 toggle @BeforeClass(alwaysRun = true)
35    public void setUpJvOptionPane()
36    {
37  1 JvOptionPane.setInteractiveMode(false);
38  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
39    }
40   
 
41  1 toggle @Test(groups = "Functional")
42    public void testIsValidReference() throws Exception
43    {
44  1 EnsemblSequenceFetcher esq = new EnsemblProtein();
45  1 Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
46  1 Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
47  1 Assert.assertFalse(esq.isValidReference("ENST00000288602"));
48  1 Assert.assertFalse(esq.isValidReference("ENSG00000288602"));
49    // non-human species having a 3 character identifier included:
50  1 Assert.assertTrue(esq.isValidReference("ENSMUSP00000099398"));
51    }
52   
 
53  1 toggle @Test(groups = "Functional")
54    public void testGetAccesionIdFromQuery() throws Exception
55    {
56  1 EnsemblSequenceFetcher esq = new EnsemblProtein();
57  1 assertEquals("ENSP00000288602",
58    esq.getAccessionIdFromQuery("ENSP00000288602"));
59  1 assertEquals("ENSMUSP00000288602",
60    esq.getAccessionIdFromQuery("ENSMUSP00000288602"));
61   
62    // ENST converted to ENSP
63  1 assertEquals("ENSP00000288602",
64    esq.getAccessionIdFromQuery("ENST00000288602"));
65  1 assertEquals("ENSMUSP00000288602",
66    esq.getAccessionIdFromQuery("ENSMUST00000288602"));
67   
68    // with valid separator:
69  1 assertEquals("ENSP00000288604",
70    esq.getAccessionIdFromQuery("ENSP00000288604 ENSP00000288602"));
71   
72    // with wrong separator:
73  1 assertEquals("ENSP00000288604,ENSP00000288602",
74    esq.getAccessionIdFromQuery("ENSP00000288604,ENSP00000288602"));
75    }
76   
77    }