JAL-1681 show cDNA consensus on protein alignment - first version

[jalview.git] / test / jalview / datamodel / AlignmentTest.java

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 3b3d926..df98af9 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -171,21 +171,27 @@ public class AlignmentTest
   }
 
   /**
-   * Aligning protein from cDNA yet to be implemented, does nothing.
+   * Aligning protein from cDNA.
    * 
    * @throws IOException
    */
   @Test
   public void testAlignAs_proteinAsCdna() throws IOException
   {
+    // see also AlignmentUtilsTests
     AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
     AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
-    String before0 = al2.getSequenceAt(0).getSequenceAsString();
-    String before1 = al2.getSequenceAt(1).getSequenceAsString();
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList ml = new MapList(new int[]
+    { 1, 12 }, new int[]
+    { 1, 4 }, 3, 1);
+    acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
+    acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
+    al2.addCodonFrame(acf);
 
     ((Alignment) al2).alignAs(al1, false, true);
-    assertEquals(before0, al2.getSequenceAt(0).getSequenceAsString());
-    assertEquals(before1, al2.getSequenceAt(1).getSequenceAsString());
+    assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
+    assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString());
   }
 
   /**