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.analysis;
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;
29 import java.util.Hashtable;
31 import org.testng.Assert;
32 import org.testng.annotations.Test;
38 public class SeqsetUtilsTest
41 * test for JAL-2046 bug - duplication of sequence features on reconstructed
44 @Test(groups = { "Functional" })
45 public void testSeqFeatureAddition()
47 SequenceI[] sqset = new SequenceI[] {
48 new Sequence("Aseq1", "AREALSEQ"),
49 new Sequence("Aseq2", "AREALSEQ") };
51 AlignmentI al = new Alignment(sqset);
53 AlignmentI ds = al.getDataset();
54 SequenceFeature sf1 = new SequenceFeature("f1", "foo", "bleh", 2, 3,
55 "far"), sf2 = new SequenceFeature("f2", "foo", "bleh", 2, 3,
57 ds.getSequenceAt(0).addSequenceFeature(sf1);
58 Hashtable unq = SeqsetUtils.uniquify(sqset, true);
59 SequenceI[] sqset2 = new SequenceI[] {
60 new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
61 new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
62 Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sf1);
63 Assert.assertEquals(sqset2[0].getSequenceFeatures(), null);
64 ds.getSequenceAt(0).addSequenceFeature(sf2);
65 Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
66 SeqsetUtils.deuniquify(unq, sqset2);
67 // explicitly test that original sequence features still exist because they
68 // are on the shared dataset sequence
69 Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
70 Assert.assertEquals(sqset2[0].getSequenceFeatures().length, 2);
71 Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sqset2[0]
72 .getSequenceFeatures()[0]);
73 Assert.assertTrue(sqset[0].getSequenceFeatures()[1] == sqset2[0]
74 .getSequenceFeatures()[1]);