JAL-1705 test updated for canonicalised UNIPROT sequence name

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

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 2520de0..e9bcf24 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -655,14 +655,17 @@ public class MapListTest
   @Test(groups = { "Functional" })
   public void testIsFromForwardStrand()
   {
+    // [3-9] declares forward strand
     MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
             new int[] { 20, 11 }, 1, 1);
     assertTrue(ml.isFromForwardStrand());
 
+    // [11-5] declares reverse strand ([13-14] is ignored)
     ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
             new int[] { 20, 11 }, 1, 1);
     assertFalse(ml.isFromForwardStrand());
 
+    // all single position ranges - defaults to forward strand
     ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
             1);
     assertTrue(ml.isFromForwardStrand());
@@ -697,6 +700,12 @@ public class MapListTest
     List<int[]> merged = MapList.coalesceRanges(ranges);
     assertEquals(1, merged.size());
     assertArrayEquals(new int[] { 1, 7 }, merged.get(0));
+    // verify input list is unchanged
+    assertEquals(4, ranges.size());
+    assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
+    assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
+    assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
+    assertArrayEquals(new int[] { 5, 7 }, ranges.get(3));
 
     // merging in reverse direction:
     ranges.clear();
@@ -723,4 +732,62 @@ public class MapListTest
     assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
     assertArrayEquals(new int[] { 12, 7 }, merged.get(1));
   }
+
+  /**
+   * Test the method that merges a list of ranges where possible
+   */
+  @Test(groups = { "Functional" })
+  public void testCoalesceRanges_withOverlap()
+  {
+    List<int[]> ranges = new ArrayList<int[]>();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 2, 5 });
+
+    /*
+     * [2, 5] should extend [1, 3]
+     */
+    List<int[]> merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
+
+    /*
+     * a subsumed interval should be dropped
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 6 });
+    ranges.add(new int[] { 2, 4 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
+
+    ranges.clear();
+    ranges.add(new int[] { 1, 5 });
+    ranges.add(new int[] { 1, 6 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
+
+    /*
+     * merge duplicate ranges
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 1, 3 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 3 }, merged.get(0));
+
+    /*
+     * reverse direction
+     */
+    ranges.clear();
+    ranges.add(new int[] { 9, 5 });
+    ranges.add(new int[] { 9, 4 });
+    ranges.add(new int[] { 8, 3 });
+    ranges.add(new int[] { 3, 2 });
+    ranges.add(new int[] { 1, 0 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
+  }
 }