JAL-1705 helper method for mapping excluding stop codon

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

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 7100381..095ab1b 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -23,6 +23,7 @@ package jalview.util;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
@@ -855,4 +856,59 @@ public class MappingUtilsTest
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
     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));
+  }
 }