JAL-1705 unit test for aligning with incomplete start codon

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 818267d..f9c1a11 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1696,4 +1696,55 @@ public class AlignmentUtilsTests
     assertEquals("[11, 17]", Arrays.toString(cdsColumns.get(2)));
     assertEquals("[19, 23]", Arrays.toString(cdsColumns.get(3)));
   }
+
+  /**
+   * Test the method that realigns protein to match mapped codon alignment.
+   */
+  @Test(groups = { "Functional" })
+  public void testAlignProteinAsDna_incompleteStartCodon()
+  {
+    // seq1: incomplete start codon (not mapped), then [3, 11]
+    SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
+    // seq2 codons are [4, 5], [8, 11]
+    SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
+    // seq3 incomplete start codon at 'tt'
+    SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+    dna.setDataset(null);
+  
+    // prot1 has 'X' for incomplete start codon (not mapped)
+    SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
+    SequenceI prot2 = new Sequence("Seq2", "NG");
+    SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
+    AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
+        prot3 });
+    protein.setDataset(null);
+  
+    // map dna1 [3, 11] to prot1 [2, 4] KFG
+    MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
+
+    // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
+    map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
+    acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
+
+    // map dna3 [9, 11] to prot3 [2, 2] G
+    map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
+    acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
+
+    ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
+    acfs.add(acf);
+    protein.setCodonFrames(acfs);
+
+    /*
+     * verify X is included in the aligned proteins, and placed just
+     * before the first mapped residue 
+     * CCT is between CCC and TTT
+     */
+    AlignmentUtils.alignProteinAsDna(protein, dna);
+    assertEquals("XK-FG", prot1.getSequenceAsString());
+    assertEquals("--N-G", prot2.getSequenceAsString());
+    assertEquals("---XG", prot3.getSequenceAsString());
+  }
 }