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

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

diff --git a/test/jalview/schemes/DnaCodonTests.java b/test/jalview/schemes/DnaCodonTests.java
index 3d025a8..45b56c2 100644 (file)
--- a/test/jalview/schemes/DnaCodonTests.java
+++ b/test/jalview/schemes/DnaCodonTests.java
@@ -1,66 +1,58 @@
+/*
+ * 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.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
-  public void testAmbiguityCodon() {
-    for (String ac:ResidueProperties.ambiguityCodes.keySet())
-    {
-      assertTrue("Couldn't resolve GGN as glycine codon",ResidueProperties.codonHash2.get("GG"+ac).equals("G"));
-    }
+    assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
   }
-  @Test
-  public void regenerateCodonTable() {
-    for (Map.Entry<String, String> codon:ResidueProperties.codonHash2.entrySet())
+
+  @Test(groups = { "Functional" })
+  public void testAmbiguityCodon()
+  {
+    for (String ac : ResidueProperties.ambiguityCodes.keySet())
     {
-      System.out.println("ResidueProperties.codonHash2.set(\""+codon.getKey()+"\", \""+codon.getValue()+"\");");
+      assertTrue("Couldn't resolve GGN as glycine codon",
+              ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
     }
   }
-  @Test
-  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())
+
+  @Test(groups = { "Functional" })
+  public void regenerateCodonTable()
+  {
+    for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
+            .entrySet())
     {
-      String amacid=(String) aa;
-      for (Object codons:((Vector)ResidueProperties.codonHash.get(amacid)))
-      {
-        String codon = (String) codons;
-        String trans = ResidueProperties.codonTranslate(codon);
-        String oldtrans = ResidueProperties._codonTranslate(codon);
-        if (trans==null) {
-          additional+="\nOld translation table includes additional codons for "+amacid+" : "+codon;
-        }
-        if (oldtrans==null) {
-          failtrans+=("\nold translation routine failed for old translation entry (aa was "+amacid+" codon was "+codon+")");
-        }
-        if (!oldtrans.equals(trans))
-        {
-          differentTr+=("\nDifferent translation for old and new routines: "+amacid+" "+codon+" => expected "+oldtrans+" and got "+trans);
-        }
-      }
+      System.out.println("ResidueProperties.codonHash2.set(\""
+              + codon.getKey() + "\", \"" + codon.getValue() + "\");");
     }
-    assertTrue(""+additional+"\n"+failtrans+"\n"+differentTr,additional.length()==0 && failtrans.length()==0 && differentTr.length()==0);
   }
 }