+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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 org.testng.annotations.Test;
+
import java.util.Arrays;
+import org.testng.annotations.Test;
+
public class CodingUtilsTest
{
- @Test
+ @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)));
+ 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
+ @Test(groups = { "Functional" })
public void testDecodeNucleotide()
{
assertEquals('A', CodingUtils.decodeNucleotide(0));
assertEquals('0', CodingUtils.decodeNucleotide(4));
}
- @Test
+ @Test(groups = { "Functional" })
public void testEncodeCodon()
{
assertTrue(CodingUtils.encodeCodon('Z') < 0);
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' }));
+ 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' }));
}
}