JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / test / jalview / analysis / CodingUtilsTest.java

diff --git a/test/jalview/analysis/CodingUtilsTest.java b/test/jalview/analysis/CodingUtilsTest.java
index a4b6c3f..38ee3fe 100644 (file)
--- a/test/jalview/analysis/CodingUtilsTest.java
+++ b/test/jalview/analysis/CodingUtilsTest.java
@@ -1,35 +1,57 @@
+/*
+ * 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 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));
@@ -39,7 +61,7 @@ public class CodingUtilsTest
     assertEquals('0', CodingUtils.decodeNucleotide(4));
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testEncodeCodon()
   {
     assertTrue(CodingUtils.encodeCodon('Z') < 0);
@@ -53,24 +75,16 @@ public class CodingUtilsTest
     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' }));
   }
 
 }