JAL-1793 spike branch updated to latest

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index d229a39..1bff8bf 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -64,6 +64,8 @@ import org.testng.annotations.Test;
 
 public class AlignmentUtilsTests
 {
+  private static Sequence ts = new Sequence("short",
+          "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -72,9 +74,6 @@ public class AlignmentUtilsTests
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  private static Sequence ts = new Sequence("short",
-          "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
-
   @Test(groups = { "Functional" })
   public void testExpandContext()
   {
@@ -2633,4 +2632,71 @@ public class AlignmentUtilsTests
     assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
             toMap.toString());
   }
+
+  /**
+   * Tests for the method that maps nucleotide to protein based on CDS features
+   */
+  @Test(groups = "Functional")
+  public void testMapCdsToProtein()
+  {
+    SequenceI peptide = new Sequence("pep", "KLQ");
+
+    /*
+     * Case 1: CDS 3 times length of peptide
+     * NB method only checks lengths match, not translation
+     */
+    SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
+    dna.createDatasetSequence();
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
+    MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+    assertEquals(3, ml.getFromRatio());
+    assertEquals(1, ml.getToRatio());
+    assertEquals("[[1, 3]]",
+            Arrays.deepToString(ml.getToRanges().toArray()));
+    assertEquals("[[1, 4], [9, 13]]",
+            Arrays.deepToString(ml.getFromRanges().toArray()));
+
+    /*
+     * Case 2: CDS 3 times length of peptide + stop codon
+     * (note code does not currently check trailing codon is a stop codon)
+     */
+    dna = new Sequence("dna", "AACGacgtCTCCTTGA");
+    dna.createDatasetSequence();
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
+    ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+    assertEquals(3, ml.getFromRatio());
+    assertEquals(1, ml.getToRatio());
+    assertEquals("[[1, 3]]",
+            Arrays.deepToString(ml.getToRanges().toArray()));
+    assertEquals("[[1, 4], [9, 13]]",
+            Arrays.deepToString(ml.getFromRanges().toArray()));
+
+    /*
+     * Case 3: CDS not 3 times length of peptide - no mapping is made
+     */
+    dna = new Sequence("dna", "AACGacgtCTCCTTG");
+    dna.createDatasetSequence();
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
+    ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+    assertNull(ml);
+
+    /*
+     * Case 4: incomplete start codon corresponding to X in peptide
+     */
+    dna = new Sequence("dna", "ACGacgtCTCCTTGG");
+    dna.createDatasetSequence();
+    SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
+    sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
+    dna.addSequenceFeature(sf);
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
+    peptide = new Sequence("pep", "XLQ");
+    ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+    assertEquals("[[2, 3]]",
+            Arrays.deepToString(ml.getToRanges().toArray()));
+    assertEquals("[[3, 3], [8, 12]]",
+            Arrays.deepToString(ml.getFromRanges().toArray()));
+  }
 }