JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / test / jalview / schemes / DnaCodonTests.java

diff --git a/test/jalview/schemes/DnaCodonTests.java b/test/jalview/schemes/DnaCodonTests.java
index 6791d7c..07ae7bb 100644 (file)
--- a/test/jalview/schemes/DnaCodonTests.java
+++ b/test/jalview/schemes/DnaCodonTests.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,31 +20,22 @@
  */
 package jalview.schemes;
 
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
-import java.io.IOException;
 import java.util.Map;
-import java.util.Vector;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 public class DnaCodonTests
 {
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testAmbiguityCodeGeneration()
   {
     assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testAmbiguityCodon()
   {
     for (String ac : ResidueProperties.ambiguityCodes.keySet())
@@ -54,7 +45,7 @@ public class DnaCodonTests
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void regenerateCodonTable()
   {
     for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
@@ -65,19 +56,16 @@ public class DnaCodonTests
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void checkOldCodonagainstNewCodonTable()
   {
     // note - this test will be removed once the old codon table (including
     // Vectors) is removed
     String additional = "", failtrans = "", differentTr = "";
-    for (Object aa : ResidueProperties.codonHash.keySet())
+    for (String amacid : ResidueProperties.codonHash.keySet())
     {
-      String amacid = (String) aa;
-      for (Object codons : ((Vector) ResidueProperties.codonHash
-              .get(amacid)))
+      for (String codon : ResidueProperties.codonHash.get(amacid))
       {
-        String codon = (String) codons;
         String trans = ResidueProperties.codonTranslate(codon);
         String oldtrans = ResidueProperties._codonTranslate(codon);
         if (trans == null)