X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FDnaCodonTests.java;h=3d025a8455091cf532f229a29057a1fd5325ffcf;hb=304c9952d6c35c0740428d8dec3761b640bede14;hp=690a7bcc4565b50f326b2c7638545f297b06e37a;hpb=fbaefbc8965071fd362e9f47aa3d855dcdf312e9;p=jalview.git

diff --git a/test/jalview/schemes/DnaCodonTests.java b/test/jalview/schemes/DnaCodonTests.java
index 690a7bc..3d025a8 100644
--- a/test/jalview/schemes/DnaCodonTests.java
+++ b/test/jalview/schemes/DnaCodonTests.java
@@ -9,6 +9,7 @@ import jalview.datamodel.SequenceI;
 
 import java.io.IOException;
 import java.util.Map;
+import java.util.Vector;
 
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
@@ -17,16 +18,6 @@ import org.junit.Test;
 public class DnaCodonTests
 {
 
-  @BeforeClass
-  public static void setUpBeforeClass() throws Exception
-  {
-  }
-
-  @AfterClass
-  public static void tearDownAfterClass() throws Exception
-  {
-  }
-
   @Test
   public void testAmbiguityCodeGeneration()
   {
@@ -46,4 +37,30 @@ public class DnaCodonTests
       System.out.println("ResidueProperties.codonHash2.set(\""+codon.getKey()+"\", \""+codon.getValue()+"\");");
     }
   }
+  @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())
+    {
+      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);
+        }
+      }
+    }
+    assertTrue(""+additional+"\n"+failtrans+"\n"+differentTr,additional.length()==0 && failtrans.length()==0 && differentTr.length()==0);
+  }
 }