JAL-1260 file formats and IdentifyFile updates for GenBank and ENA
[jalview.git] / test / jalview / analysis / SeqsetUtilsTest.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 
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   @BeforeClass(alwaysRun = true)
44   public void setUpJvOptionPane()
45   {
46     JvOptionPane.setInteractiveMode(false);
47     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48   }
49
50
51   /**
52    * test for JAL-2046 bug - duplication of sequence features on reconstructed
53    * alignment
54    */
55   @Test(groups = { "Functional" })
56   public void testSeqFeatureAddition()
57   {
58     SequenceI[] sqset = new SequenceI[] {
59         new Sequence("Aseq1", "AREALSEQ"),
60         new Sequence("Aseq2", "AREALSEQ") };
61
62     AlignmentI al = new Alignment(sqset);
63     al.setDataset(null);
64     AlignmentI ds = al.getDataset();
65     SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
66     SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
67     ds.getSequenceAt(0).addSequenceFeature(sf1);
68     Hashtable unq = SeqsetUtils.uniquify(sqset, true);
69     SequenceI[] sqset2 = new SequenceI[] {
70         new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
71         new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
72     Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
73     Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
74     ds.getSequenceAt(0).addSequenceFeature(sf2);
75     Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
76     SeqsetUtils.deuniquify(unq, sqset2);
77     // explicitly test that original sequence features still exist because they
78     // are on the shared dataset sequence
79     Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
80     Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
81     Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sqset2[0]
82             .getSequenceFeatures().get(0));
83     Assert.assertSame(sqset[0].getSequenceFeatures().get(1), sqset2[0]
84             .getSequenceFeatures().get(1));
85   }
86 }