JAL-1517 source formatting

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

diff --git a/test/jalview/schemes/DnaCodonTests.java b/test/jalview/schemes/DnaCodonTests.java
index 664d2d2..d8529f8 100644 (file)
--- a/test/jalview/schemes/DnaCodonTests.java
+++ b/test/jalview/schemes/DnaCodonTests.java
@@ -41,46 +41,69 @@ public class DnaCodonTests
   @Test
   public void testAmbiguityCodeGeneration()
   {
-    assertTrue(ResidueProperties.ambiguityCodes.size()>0);
+    assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
   }
+
   @Test
-  public void testAmbiguityCodon() {
-    for (String ac:ResidueProperties.ambiguityCodes.keySet())
+  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("Couldn't resolve GGN as glycine codon",
+              ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
     }
   }
+
   @Test
-  public void regenerateCodonTable() {
-    for (Map.Entry<String, String> codon:ResidueProperties.codonHash2.entrySet())
+  public void regenerateCodonTable()
+  {
+    for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
+            .entrySet())
     {
-      System.out.println("ResidueProperties.codonHash2.set(\""+codon.getKey()+"\", \""+codon.getValue()+"\");");
+      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())
+  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 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 (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 == 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);
+          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);
+    assertTrue("" + additional + "\n" + failtrans + "\n" + differentTr,
+            additional.length() == 0 && failtrans.length() == 0
+                    && differentTr.length() == 0);
   }
 }