+
+ /**
+ * Test that method that inspects for the (first) forward or reverse from
+ * range. Single position ranges are ignored.
+ */
+ @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());
+ }
+
+ /**
+ * Test the method that merges a list of ranges where possible
+ */
+ @Test(groups = { "Functional" })
+ public void testCoalesceRanges()
+ {
+ assertNull(MapList.coalesceRanges(null));
+ List<int[]> ranges = new ArrayList<int[]>();
+ assertSame(ranges, MapList.coalesceRanges(ranges));
+ ranges.add(new int[] { 1, 3 });
+ assertSame(ranges, MapList.coalesceRanges(ranges));
+
+ // add non-contiguous range:
+ ranges.add(new int[] { 5, 6 });
+ assertSame(ranges, MapList.coalesceRanges(ranges));
+
+ // 'contiguous' range in opposite direction is not merged:
+ ranges.add(new int[] { 7, 6 });
+ assertSame(ranges, MapList.coalesceRanges(ranges));
+
+ // merging in forward direction:
+ ranges.clear();
+ ranges.add(new int[] { 1, 3 });
+ ranges.add(new int[] { 4, 5 });
+ ranges.add(new int[] { 5, 5 });
+ ranges.add(new int[] { 5, 7 });
+ 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();
+ ranges.add(new int[] { 7, 5 });
+ ranges.add(new int[] { 5, 4 });
+ ranges.add(new int[] { 4, 4 });
+ ranges.add(new int[] { 3, 1 });
+ merged = MapList.coalesceRanges(ranges);
+ assertEquals(1, merged.size());
+ assertArrayEquals(new int[] { 7, 1 }, merged.get(0));
+
+ // merging with switches of direction:
+ ranges.clear();
+ ranges.add(new int[] { 1, 3 });
+ ranges.add(new int[] { 4, 5 });
+ ranges.add(new int[] { 5, 5 });
+ ranges.add(new int[] { 6, 6 });
+ ranges.add(new int[] { 12, 10 });
+ ranges.add(new int[] { 9, 8 });
+ ranges.add(new int[] { 8, 8 });
+ ranges.add(new int[] { 7, 7 });
+ merged = MapList.coalesceRanges(ranges);
+ assertEquals(2, merged.size());
+ 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));
+ }