1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.analysis

File SeqsetUtilsTest.java

 

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SeqsetUtilsTest 40 20 2
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Contributing tests

This file is covered by 1 test. .

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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.analysis;
22   
23    import jalview.datamodel.Alignment;
24    import jalview.datamodel.AlignmentI;
25    import jalview.datamodel.Sequence;
26    import jalview.datamodel.SequenceFeature;
27    import jalview.datamodel.SequenceI;
28    import jalview.gui.JvOptionPane;
29   
30    import java.util.Hashtable;
31   
32    import org.testng.Assert;
33    import org.testng.annotations.BeforeClass;
34    import org.testng.annotations.Test;
35   
36    /**
37    * @author jprocter
38    *
39    */
 
40    public class SeqsetUtilsTest
41    {
42   
 
43  1 toggle @BeforeClass(alwaysRun = true)
44    public void setUpJvOptionPane()
45    {
46  1 JvOptionPane.setInteractiveMode(false);
47  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48    }
49   
50    /**
51    * test for JAL-2046 bug - duplication of sequence features on reconstructed
52    * alignment
53    */
 
54  1 toggle @Test(groups = { "Functional" })
55    public void testSeqFeatureAddition()
56    {
57  1 SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"),
58    new Sequence("Aseq2", "AREALSEQ") };
59   
60  1 AlignmentI al = new Alignment(sqset);
61  1 al.setDataset(null);
62  1 AlignmentI ds = al.getDataset();
63  1 SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
64  1 SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
65  1 ds.getSequenceAt(0).addSequenceFeature(sf1);
66  1 Hashtable unq = SeqsetUtils.uniquify(sqset, true);
67  1 SequenceI[] sqset2 = new SequenceI[] {
68    new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
69    new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
70  1 Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
71  1 Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
72  1 ds.getSequenceAt(0).addSequenceFeature(sf2);
73  1 Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
74  1 SeqsetUtils.deuniquify(unq, sqset2);
75    // explicitly test that original sequence features still exist because they
76    // are on the shared dataset sequence
77  1 Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
78  1 Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
79  1 Assert.assertSame(sqset[0].getSequenceFeatures().get(0),
80    sqset2[0].getSequenceFeatures().get(0));
81  1 Assert.assertSame(sqset[0].getSequenceFeatures().get(1),
82    sqset2[0].getSequenceFeatures().get(1));
83    }
84    }