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