MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
assertTrue(ml.equals(ml));
+ assertEquals(ml.hashCode(), ml.hashCode());
assertTrue(ml.equals(ml1));
+ assertEquals(ml.hashCode(), ml1.hashCode());
assertTrue(ml1.equals(ml));
assertFalse(ml.equals(null));
@Test(groups = { "Functional" })
public void testGetRanges()
{
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
ranges.add(new int[] { 2, 3 });
ranges.add(new int[] { 5, 6 });
assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
}
- @Test(groups = "Functional")
- public void testAddRange()
- {
- int[] range = { 1, 5 };
- List<int[]> ranges = new ArrayList<int[]>();
-
- // add to empty list:
- MapList.addRange(range, ranges);
- assertEquals(1, ranges.size());
- assertSame(range, ranges.get(0));
-
- // extend contiguous (same position):
- MapList.addRange(new int[] { 5, 10 }, ranges);
- assertEquals(1, ranges.size());
- assertEquals(1, ranges.get(0)[0]);
- assertEquals(10, ranges.get(0)[1]);
-
- // extend contiguous (next position):
- MapList.addRange(new int[] { 11, 15 }, ranges);
- assertEquals(1, ranges.size());
- assertEquals(1, ranges.get(0)[0]);
- assertEquals(15, ranges.get(0)[1]);
-
- // change direction: range is not merged:
- MapList.addRange(new int[] { 16, 10 }, ranges);
- assertEquals(2, ranges.size());
- assertEquals(16, ranges.get(1)[0]);
- assertEquals(10, ranges.get(1)[1]);
-
- // extend reverse contiguous (same position):
- MapList.addRange(new int[] { 10, 8 }, ranges);
- assertEquals(2, ranges.size());
- assertEquals(16, ranges.get(1)[0]);
- assertEquals(8, ranges.get(1)[1]);
-
- // extend reverse contiguous (next position):
- MapList.addRange(new int[] { 7, 6 }, ranges);
- assertEquals(2, ranges.size());
- assertEquals(16, ranges.get(1)[0]);
- assertEquals(6, ranges.get(1)[1]);
-
- // change direction: range is not merged:
- MapList.addRange(new int[] { 6, 9 }, ranges);
- assertEquals(3, ranges.size());
- assertEquals(6, ranges.get(2)[0]);
- assertEquals(9, ranges.get(2)[1]);
-
- // not contiguous: not merged
- MapList.addRange(new int[] { 11, 12 }, ranges);
- assertEquals(4, ranges.size());
- assertEquals(11, ranges.get(3)[0]);
- assertEquals(12, ranges.get(3)[1]);
- }
-
/**
* Check state after construction
*/
public void testCoalesceRanges()
{
assertNull(MapList.coalesceRanges(null));
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
assertSame(ranges, MapList.coalesceRanges(ranges));
ranges.add(new int[] { 1, 3 });
assertSame(ranges, MapList.coalesceRanges(ranges));
@Test(groups = { "Functional" })
public void testCoalesceRanges_withOverlap()
{
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
ranges.add(new int[] { 1, 3 });
ranges.add(new int[] { 2, 5 });
compound = ml1.traverse(ml2);
assertNull(compound);
}
+
+ /**
+ * Test that method that inspects for the (first) forward or reverse 'to' range.
+ * Single position ranges are ignored.
+ */
+ @Test(groups = { "Functional" })
+ public void testIsToForwardsStrand()
+ {
+ // [3-9] declares forward strand
+ MapList ml = new MapList(new int[] { 20, 11 },
+ new int[]
+ { 2, 2, 3, 9, 12, 11 }, 1, 1);
+ assertTrue(ml.isToForwardStrand());
+
+ // [11-5] declares reverse strand ([13-14] is ignored)
+ ml = new MapList(new int[] { 20, 11 },
+ new int[]
+ { 2, 2, 11, 5, 13, 14 }, 1, 1);
+ assertFalse(ml.isToForwardStrand());
+
+ // all single position ranges - defaults to forward strand
+ ml = new MapList(new int[] { 3, 1 }, new int[] { 2, 2, 4, 4, 6, 6 }, 1,
+ 1);
+ assertTrue(ml.isToForwardStrand());
+ }
}