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 static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertTrue;
26 import java.util.Arrays;
28 import org.testng.annotations.Test;
30 public class CodingUtilsTest
33 @Test(groups = { "Functional" })
34 public void testDecodeCodon()
36 assertTrue(Arrays.equals(new char[] { 'A', 'A', 'A' },
37 CodingUtils.decodeCodon(0)));
38 assertTrue(Arrays.equals(new char[] { 'A', 'A', 'C' },
39 CodingUtils.decodeCodon(1)));
40 assertTrue(Arrays.equals(new char[] { 'A', 'A', 'G' },
41 CodingUtils.decodeCodon(2)));
42 assertTrue(Arrays.equals(new char[] { 'A', 'A', 'T' },
43 CodingUtils.decodeCodon(3)));
44 assertTrue(Arrays.equals(new char[] { 'A', 'C', 'A' },
45 CodingUtils.decodeCodon(4)));
46 assertTrue(Arrays.equals(new char[] { 'C', 'A', 'A' },
47 CodingUtils.decodeCodon(16)));
48 assertTrue(Arrays.equals(new char[] { 'G', 'G', 'G' },
49 CodingUtils.decodeCodon(42)));
50 assertTrue(Arrays.equals(new char[] { 'T', 'T', 'T' },
51 CodingUtils.decodeCodon(63)));
54 @Test(groups = { "Functional" })
55 public void testDecodeNucleotide()
57 assertEquals('A', CodingUtils.decodeNucleotide(0));
58 assertEquals('C', CodingUtils.decodeNucleotide(1));
59 assertEquals('G', CodingUtils.decodeNucleotide(2));
60 assertEquals('T', CodingUtils.decodeNucleotide(3));
61 assertEquals('0', CodingUtils.decodeNucleotide(4));
64 @Test(groups = { "Functional" })
65 public void testEncodeCodon()
67 assertTrue(CodingUtils.encodeCodon('Z') < 0);
68 assertEquals(0, CodingUtils.encodeCodon('a'));
69 assertEquals(0, CodingUtils.encodeCodon('A'));
70 assertEquals(1, CodingUtils.encodeCodon('c'));
71 assertEquals(1, CodingUtils.encodeCodon('C'));
72 assertEquals(2, CodingUtils.encodeCodon('g'));
73 assertEquals(2, CodingUtils.encodeCodon('G'));
74 assertEquals(3, CodingUtils.encodeCodon('t'));
75 assertEquals(3, CodingUtils.encodeCodon('T'));
76 assertEquals(3, CodingUtils.encodeCodon('u'));
77 assertEquals(3, CodingUtils.encodeCodon('U'));
79 assertEquals(-1, CodingUtils.encodeCodon(null));
80 assertEquals(0, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'A' }));
81 assertEquals(1, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'C' }));
82 assertEquals(2, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'G' }));
83 assertEquals(3, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'T' }));
84 assertEquals(4, CodingUtils.encodeCodon(new char[] { 'A', 'C', 'A' }));
85 assertEquals(16, CodingUtils.encodeCodon(new char[] { 'C', 'A', 'A' }));
86 assertEquals(42, CodingUtils.encodeCodon(new char[] { 'G', 'G', 'G' }));
87 assertEquals(63, CodingUtils.encodeCodon(new char[] { 'T', 'T', 'T' }));