JAL-1705 include stop codons in derived CDS; support ensemblgenomes

[jalview.git] / test / jalview / util / MappingUtilsTest.java

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 3c4d4f8..853ebd5 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -858,61 +858,6 @@ public class MappingUtilsTest
     assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
   }
 
-  /**
-   * Tests for the method that removes the trailing stop codon from a mapping
-   * range i.e. the last 3 positions (whether split or not)
-   */
-  @Test(groups = { "Functional" })
-  public void testUnmapStopCodon()
-  {
-    List<int[]> ranges = new ArrayList<int[]>();
-
-    // simple case, forward strand:
-    ranges.add(new int[] { 1, 3 });
-    ranges.add(new int[] { 9, 14 });
-    MappingUtils.unmapStopCodon(ranges, 9);
-    assertEquals(2, ranges.size());
-    assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
-    assertArrayEquals(new int[] { 9, 11 }, ranges.get(1));
-
-    // split stop codon, forward strand:
-    ranges.clear();
-    ranges.add(new int[] { 1, 8 });
-    ranges.add(new int[] { 10, 10 });
-    MappingUtils.unmapStopCodon(ranges, 9);
-    assertEquals(1, ranges.size());
-    assertArrayEquals(new int[] { 1, 6 }, ranges.get(0));
-
-    // very split stop codon, forward strand:
-    ranges.clear();
-    ranges.add(new int[] { 1, 1 });
-    ranges.add(new int[] { 3, 4 });
-    ranges.add(new int[] { 6, 6 });
-    ranges.add(new int[] { 8, 8 });
-    ranges.add(new int[] { 10, 10 });
-    MappingUtils.unmapStopCodon(ranges, 6);
-    assertEquals(2, ranges.size());
-    assertArrayEquals(new int[] { 1, 1 }, ranges.get(0));
-    assertArrayEquals(new int[] { 3, 4 }, ranges.get(1));
-
-    // simple case, reverse strand:
-    ranges.clear();
-    ranges.add(new int[] { 12, 10 });
-    ranges.add(new int[] { 6, 1 });
-    MappingUtils.unmapStopCodon(ranges, 9);
-    assertEquals(2, ranges.size());
-    assertArrayEquals(new int[] { 12, 10 }, ranges.get(0));
-    assertArrayEquals(new int[] { 6, 4 }, ranges.get(1));
-
-    // split stop codon, reverse strand:
-    ranges.clear();
-    ranges.add(new int[] { 12, 6 });
-    ranges.add(new int[] { 4, 3 });
-    MappingUtils.unmapStopCodon(ranges, 9);
-    assertEquals(1, ranges.size());
-    assertArrayEquals(new int[] { 12, 7 }, ranges.get(0));
-  }
-
   @Test(groups = { "Functional" })
   public void testGetLength()
   {