+ intervals.add(new int[] { 30, 30 });
+ assertArrayEquals(new int[] { 29, 1 },
+ MapList.countPositions(intervals, 30));
+
+ /*
+ * it is the first matched occurrence that is returned
+ */
+ intervals.clear();
+ intervals.add(new int[] { 1, 2 });
+ intervals.add(new int[] { 2, 3 });
+ assertArrayEquals(new int[] { 2, 1 },
+ MapList.countPositions(intervals, 2));
+ intervals.add(new int[] { -1, -2 });
+ intervals.add(new int[] { -2, -3 });
+ assertArrayEquals(new int[] { 6, -1 },
+ MapList.countPositions(intervals, -2));
+ }
+
+ /**
+ * Tests for helper method that adds any overlap (plus offset) to a set of
+ * overlaps
+ */
+ @Test(groups = { "Functional" })
+ public void testAddOffsetPositions()
+ {
+ List<int[]> mapped = new ArrayList<>();
+ int[] range = new int[] { 10, 20 };
+ BitSet offsets = new BitSet();
+
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // nothing marked for overlap
+
+ offsets.set(11);
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // no offset 11 in range
+
+ offsets.set(4, 6); // this sets bits 4 and 5
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertEquals(1, mapped.size());
+ assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
+
+ mapped.clear();
+ offsets.set(10);
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
+ assertArrayEquals(new int[] { 20, 20 }, mapped.get(1));
+
+ /*
+ * reverse range
+ */
+ range = new int[] { 20, 10 };
+ mapped.clear();
+ offsets.clear();
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // nothing marked for overlap
+ offsets.set(11);
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // no offset 11 in range
+ offsets.set(0);
+ offsets.set(10);
+ offsets.set(6, 8); // sets bits 6 and 7
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertEquals(3, mapped.size());
+ assertArrayEquals(new int[] { 20, 20 }, mapped.get(0));
+ assertArrayEquals(new int[] { 14, 13 }, mapped.get(1));
+ assertArrayEquals(new int[] { 10, 10 }, mapped.get(2));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetPositionsForOffsets()
+ {
+ List<int[]> ranges = new ArrayList<>();
+ BitSet offsets = new BitSet();
+ List<int[]> mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertTrue(mapped.isEmpty()); // no ranges and no offsets!
+
+ offsets.set(5, 1000);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertTrue(mapped.isEmpty()); // no ranges
+
+ /*
+ * one range with overlap of offsets
+ */
+ ranges.add(new int[] { 15, 25 });
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(1, mapped.size());
+ assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
+
+ /*
+ * two ranges
+ */
+ ranges.add(new int[] { 300, 320 });
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
+ assertArrayEquals(new int[] { 300, 320 }, mapped.get(1));
+
+ /*
+ * boundary case - right end of first range overlaps
+ */
+ offsets.clear();
+ offsets.set(10);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(1, mapped.size());
+ assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
+
+ /*
+ * boundary case - left end of second range overlaps
+ */
+ offsets.set(11);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
+ assertArrayEquals(new int[] { 300, 300 }, mapped.get(1));
+
+ /*
+ * offsets into a circular range are reported in
+ * the order in which they are traversed
+ */
+ ranges.clear();
+ ranges.add(new int[] { 100, 150 });
+ ranges.add(new int[] { 60, 80 });
+ offsets.clear();
+ offsets.set(45, 55); // sets bits 45 to 54
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 145, 150 }, mapped.get(0)); // offsets 45-50
+ assertArrayEquals(new int[] { 60, 63 }, mapped.get(1)); // offsets 51-54
+
+ /*
+ * reverse range overlap is reported with start < end
+ */
+ ranges.clear();
+ ranges.add(new int[] { 4321, 4000 });
+ offsets.clear();
+ offsets.set(20, 22); // sets bits 20 and 21
+ offsets.set(30);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 4301, 4300 }, mapped.get(0));
+ assertArrayEquals(new int[] { 4291, 4291 }, mapped.get(1));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetMappedOffsetsForPositions()
+ {
+ /*
+ * start by verifying the examples in the method's Javadoc!
+ */
+ List<int[]> ranges = new ArrayList<>();
+ ranges.add(new int[] { 10, 20 });
+ ranges.add(new int[] { 31, 40 });
+ BitSet overlaps = MapList.getMappedOffsetsForPositions(1, 9, ranges, 1,
+ 1);
+ assertTrue(overlaps.isEmpty());
+ overlaps = MapList.getMappedOffsetsForPositions(1, 11, ranges, 1, 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(0));
+ assertTrue(overlaps.get(1));
+ overlaps = MapList.getMappedOffsetsForPositions(15, 35, ranges, 1, 1);
+ assertEquals(11, overlaps.cardinality());
+ for (int i = 5; i <= 11; i++)
+ {
+ assertTrue(overlaps.get(i));
+ }
+
+ ranges.clear();
+ ranges.add(new int[] { 1, 200 });
+ overlaps = MapList.getMappedOffsetsForPositions(9, 9, ranges, 1, 3);
+ assertEquals(3, overlaps.cardinality());
+ assertTrue(overlaps.get(24));
+ assertTrue(overlaps.get(25));
+ assertTrue(overlaps.get(26));
+
+ ranges.clear();
+ ranges.add(new int[] { 101, 150 });
+ ranges.add(new int[] { 171, 180 });
+ overlaps = MapList.getMappedOffsetsForPositions(101, 102, ranges, 3, 1);
+ assertEquals(1, overlaps.cardinality());
+ assertTrue(overlaps.get(0));
+ overlaps = MapList.getMappedOffsetsForPositions(150, 171, ranges, 3, 1);
+ assertEquals(1, overlaps.cardinality());
+ assertTrue(overlaps.get(16));
+
+ ranges.clear();
+ ranges.add(new int[] { 101, 150 });
+ ranges.add(new int[] { 21, 30 });
+ overlaps = MapList.getMappedOffsetsForPositions(24, 40, ranges, 3, 1);
+ assertEquals(3, overlaps.cardinality());
+ assertTrue(overlaps.get(17));
+ assertTrue(overlaps.get(18));
+ assertTrue(overlaps.get(19));
+
+ /*
+ * reverse range 1:1 (e.g. reverse strand gene to transcript)
+ */
+ ranges.clear();
+ ranges.add(new int[] { 20, 10 });
+ overlaps = MapList.getMappedOffsetsForPositions(12, 13, ranges, 1, 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(7));
+ assertTrue(overlaps.get(8));
+
+ /*
+ * reverse range 3:1 (e.g. reverse strand gene to peptide)
+ * from EMBL:J03321 to P0CE20
+ */
+ ranges.clear();
+ ranges.add(new int[] { 1480, 488 });
+ overlaps = MapList.getMappedOffsetsForPositions(1460, 1460, ranges, 3,
+ 1);
+ // 1460 is the end of the 7th codon
+ assertEquals(1, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ // add one base (part codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1459, 1460, ranges, 3,
+ 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ // add second base (part codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1458, 1460, ranges, 3,
+ 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ // add third base (whole codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1457, 1460, ranges, 3,
+ 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ // add one more base (part codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1456, 1460, ranges, 3,
+ 1);
+ assertEquals(3, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ assertTrue(overlaps.get(8));