-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.analysis;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.gui.JvOptionPane;
-
-import java.util.Arrays;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class CodingUtilsTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testDecodeCodon()
- {
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'A' },
- CodingUtils.decodeCodon(0)));
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'C' },
- CodingUtils.decodeCodon(1)));
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'G' },
- CodingUtils.decodeCodon(2)));
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'T' },
- CodingUtils.decodeCodon(3)));
- assertTrue(Arrays.equals(new char[] { 'A', 'C', 'A' },
- CodingUtils.decodeCodon(4)));
- assertTrue(Arrays.equals(new char[] { 'C', 'A', 'A' },
- CodingUtils.decodeCodon(16)));
- assertTrue(Arrays.equals(new char[] { 'G', 'G', 'G' },
- CodingUtils.decodeCodon(42)));
- assertTrue(Arrays.equals(new char[] { 'T', 'T', 'T' },
- CodingUtils.decodeCodon(63)));
- }
-
- @Test(groups = { "Functional" })
- public void testDecodeNucleotide()
- {
- assertEquals('A', CodingUtils.decodeNucleotide(0));
- assertEquals('C', CodingUtils.decodeNucleotide(1));
- assertEquals('G', CodingUtils.decodeNucleotide(2));
- assertEquals('T', CodingUtils.decodeNucleotide(3));
- assertEquals('0', CodingUtils.decodeNucleotide(4));
- }
-
- @Test(groups = { "Functional" })
- public void testEncodeCodon()
- {
- assertTrue(CodingUtils.encodeCodon('Z') < 0);
- assertEquals(0, CodingUtils.encodeCodon('a'));
- assertEquals(0, CodingUtils.encodeCodon('A'));
- assertEquals(1, CodingUtils.encodeCodon('c'));
- assertEquals(1, CodingUtils.encodeCodon('C'));
- assertEquals(2, CodingUtils.encodeCodon('g'));
- assertEquals(2, CodingUtils.encodeCodon('G'));
- assertEquals(3, CodingUtils.encodeCodon('t'));
- assertEquals(3, CodingUtils.encodeCodon('T'));
- assertEquals(3, CodingUtils.encodeCodon('u'));
- assertEquals(3, CodingUtils.encodeCodon('U'));
-
- assertEquals(-1, CodingUtils.encodeCodon(null));
- assertEquals(0, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'A' }));
- assertEquals(1, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'C' }));
- assertEquals(2, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'G' }));
- assertEquals(3, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'T' }));
- assertEquals(4, CodingUtils.encodeCodon(new char[] { 'A', 'C', 'A' }));
- assertEquals(16, CodingUtils.encodeCodon(new char[] { 'C', 'A', 'A' }));
- assertEquals(42, CodingUtils.encodeCodon(new char[] { 'G', 'G', 'G' }));
- assertEquals(63, CodingUtils.encodeCodon(new char[] { 'T', 'T', 'T' }));
- }
-
-}