Merge branch 'develop' into trialMerge

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

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 6a31b31..27ae8cd 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -139,7 +139,8 @@ public class DnaTest
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     assertNotNull("Couldn't do a full width translation of test data.",
             translated);
   }
@@ -170,7 +171,8 @@ public class DnaTest
               alf.getWidth(), false);
       AlignViewportI av = new AlignViewport(alf, cs);
       Dna dna = new Dna(av, vcontigs);
-      AlignmentI transAlf = dna.translateCdna();
+      AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+              .getStandardCodeTable());
 
       assertTrue("Translation failed (ipos=" + ipos
               + ") No alignment data.", transAlf != null);
@@ -197,7 +199,8 @@ public class DnaTest
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals(
             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
@@ -222,7 +225,8 @@ public class DnaTest
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
   }
@@ -309,7 +313,8 @@ public class DnaTest
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
 
     /*
      * Jumble the cDNA sequences and translate.
@@ -325,7 +330,8 @@ public class DnaTest
     av = new AlignViewport(cdnaReordered, cs);
     contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
     dna = new Dna(av, contigs);
-    AlignmentI translated2 = dna.translateCdna();
+    AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
 
     /*
      * Check translated sequences are the same in both alignments.