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 jalview.gui.JvOptionPane;
28 import java.util.Arrays;
30 import org.testng.annotations.BeforeClass;
31 import org.testng.annotations.Test;
33 public class CodingUtilsTest
36 @BeforeClass(alwaysRun = true)
37 public void setUpJvOptionPane()
39 JvOptionPane.setInteractiveMode(false);
40 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
43 @Test(groups = { "Functional" })
44 public void testDecodeCodon()
47 Arrays.equals(new char[]
48 { 'A', 'A', 'A' }, CodingUtils.decodeCodon(0)));
50 Arrays.equals(new char[]
51 { 'A', 'A', 'C' }, CodingUtils.decodeCodon(1)));
53 Arrays.equals(new char[]
54 { 'A', 'A', 'G' }, CodingUtils.decodeCodon(2)));
56 Arrays.equals(new char[]
57 { 'A', 'A', 'T' }, CodingUtils.decodeCodon(3)));
59 Arrays.equals(new char[]
60 { 'A', 'C', 'A' }, CodingUtils.decodeCodon(4)));
62 Arrays.equals(new char[]
63 { 'C', 'A', 'A' }, CodingUtils.decodeCodon(16)));
65 Arrays.equals(new char[]
66 { 'G', 'G', 'G' }, CodingUtils.decodeCodon(42)));
68 Arrays.equals(new char[]
69 { 'T', 'T', 'T' }, CodingUtils.decodeCodon(63)));
72 @Test(groups = { "Functional" })
73 public void testDecodeNucleotide()
75 assertEquals('A', CodingUtils.decodeNucleotide(0));
76 assertEquals('C', CodingUtils.decodeNucleotide(1));
77 assertEquals('G', CodingUtils.decodeNucleotide(2));
78 assertEquals('T', CodingUtils.decodeNucleotide(3));
79 assertEquals('0', CodingUtils.decodeNucleotide(4));
82 @Test(groups = { "Functional" })
83 public void testEncodeCodon()
85 assertTrue(CodingUtils.encodeCodon('Z') < 0);
86 assertEquals(0, CodingUtils.encodeCodon('a'));
87 assertEquals(0, CodingUtils.encodeCodon('A'));
88 assertEquals(1, CodingUtils.encodeCodon('c'));
89 assertEquals(1, CodingUtils.encodeCodon('C'));
90 assertEquals(2, CodingUtils.encodeCodon('g'));
91 assertEquals(2, CodingUtils.encodeCodon('G'));
92 assertEquals(3, CodingUtils.encodeCodon('t'));
93 assertEquals(3, CodingUtils.encodeCodon('T'));
94 assertEquals(3, CodingUtils.encodeCodon('u'));
95 assertEquals(3, CodingUtils.encodeCodon('U'));
97 assertEquals(-1, CodingUtils.encodeCodon(null));
98 assertEquals(0, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'A' }));
99 assertEquals(1, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'C' }));
100 assertEquals(2, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'G' }));
101 assertEquals(3, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'T' }));
102 assertEquals(4, CodingUtils.encodeCodon(new char[] { 'A', 'C', 'A' }));
103 assertEquals(16, CodingUtils.encodeCodon(new char[] { 'C', 'A', 'A' }));
104 assertEquals(42, CodingUtils.encodeCodon(new char[] { 'G', 'G', 'G' }));
105 assertEquals(63, CodingUtils.encodeCodon(new char[] { 'T', 'T', 'T' }));