def test_lcp_child_intervals_hermans_case(self):
collation = Collation()
collation.add_plain_witness("W1", "a b c d F g h i ! K ! q r s t")
collation.add_plain_witness("W2", "a b c d F g h i ! q r s t")
collation.add_plain_witness("W3", "a b c d E g h i ! q r s t")
_, child_lcp_intervals = collation.get_lcp_intervals()
self.assertFalse(child_lcp_intervals)
def test_lcp_child_intervals_hermans_case(self):
collation = Collation()
collation.add_plain_witness("W1", "a b c d F g h i ! K ! q r s t")
collation.add_plain_witness("W2", "a b c d F g h i ! q r s t")
collation.add_plain_witness("W3", "a b c d E g h i ! q r s t")
_, child_lcp_intervals = collation.get_lcp_intervals()
self.assertFalse(child_lcp_intervals)
def test_lcp_intervals_failing_use_case_old_algorithm(self):
collation = Collation()
collation.add_plain_witness("W1", "the cat and the dog")
collation.add_plain_witness("W2", "the dog and the cat")
parent_lcp_intervals, child_lcp_intervals = collation.get_lcp_intervals()
self.assertIn((1,2), parent_lcp_intervals)
self.assertIn((3,4), parent_lcp_intervals)
self.assertIn((5,6), parent_lcp_intervals)
self.assertIn((7, 10), parent_lcp_intervals)
self.assertIn((7,8), child_lcp_intervals[7])
self.assertIn((9,10), child_lcp_intervals[7])
def test_lcp_child_intervals_darwin(self):
lcp_array = array('i', [
0, 0, 0, 96, 96, 0, 151, 9, 1, 105, 105, 0, 83, 83, 0, 95, 95, 0,
39, 39, 0, 24, 24, 0, 108, 1, 0, 232, 32, 0, 181, 39, 0, 185, 43,
1, 33, 33, 0, 159, 17, 0, 160, 18, 0, 106, 106, 0, 60, 60, 0, 171,
29, 1, 215, 15, 1, 122, 15, 1, 57, 57, 1, 153, 11, 1, 165, 23, 0,
9, 9, 1, 170, 28, 0, 214, 14, 0, 62, 62, 1, 191, 49, 0, 61, 61, 0,
148, 6, 1, 8, 8, 0, 19, 19, 0, 123, 16, 0, 75, 75, 1, 90, 90, 1,
28, 28, 0, 167, 25, 1, 112, 5, 1, 132, 25, 0, 50, 50, 0, 31, 31, 0,
77, 77, 0, 97, 97, 0, 6, 6, 0, 38, 38, 0, 63, 63, 0, 30, 30, 0, 80,
80, 0, 154, 12, 0, 145, 3, 0, 129, 22, 3, 67, 67, 0, 88, 88, 0, 45,
45, 0, 217, 17, 1, 22, 22, 0, 166, 24, 0, 25, 25, 0, 201, 1, 0,
155, 13, 1, 120, 13, 0, 175, 33, 0, 195, 53, 0, 135, 28, 0, 10, 10,
0, 147, 5, 0, 138, 31, 0, 161, 19, 1, 73, 73, 0, 198, 1, 0, 86, 86,
0, 74, 74, 1, 111, 4, 0, 210, 10, 0, 84, 84, 0, 42, 42, 0, 199, 2,
0, 119, 12, 0, 46, 46, 1, 202, 2, 0, 71, 71, 0, 40, 40, 0, 142, 0,
0, 52, 52, 0, 168, 26, 2, 113, 6, 1, 163, 21, 0, 133, 26, 0, 3, 3,
0, 186, 44, 1, 101, 101, 0, 193, 51, 2, 227, 27, 0, 107, 1, 37, 37,
1, 140, 33, 0, 1, 205, 5, 0, 47, 47, 0, 127, 20, 1, 65, 65, 0, 230,
30, 0, 41, 41, 0, 91, 91, 0, 1, 1, 0, 200, 3, 0, 156, 14, 0, 0, 76,
76, 0, 109, 2, 1, 182, 40, 0, 68, 68, 1, 14, 14, 0, 126, 19, 0, 34,
34, 1, 192, 50, 1, 85, 85, 1, 128, 21, 2, 66, 66, 1, 183, 41, 1,
220, 20, 1, 5, 5, 1, 212, 12, 2, 174, 32, 2, 226, 26, 1, 59, 59, 0,
16, 16, 0, 218, 18, 0, 23, 23, 1, 11, 11, 0, 36, 36, 1, 178, 36, 0,
51, 51, 0, 213, 13, 1, 190, 48, 0, 2, 2, 1, 222, 22, 1, 188, 46, 0,
78, 78, 0, 53, 53, 0, 197, 0, 0, 136, 29, 1, 219, 19, 1, 12, 12, 0,
114, 7, 0, 89, 89, 0, 172, 30, 2, 216, 16, 0, 21, 21, 0, 209, 9, 0,
81, 81, 0, 102, 102, 0, 134, 27, 0, 98, 98, 0, 131, 24, 0, 4, 4, 0,
35, 35, 0, 179, 37, 0, 224, 24, 0, 82, 82, 0, 72, 72, 0, 139, 32,
0, 125, 18, 0, 103, 103, 0, 121, 14, 0, 189, 47, 0, 184, 42, 0, 7,
7, 1, 17, 17, 0, 207, 7, 0, 221, 21, 0, 20, 20, 0, 196, 54, 0, 79,
79, 1, 204, 4, 1, 144, 2, 2, 94, 94, 1, 56, 56, 0, 211, 11, 1, 194,
52, 3, 228, 28, 1, 157, 15, 1, 69, 69, 1, 54, 54, 1, 115, 8, 1,
173, 31, 1, 225, 25, 1, 177, 35, 1, 100, 100, 0, 203, 3, 0, 150, 8,
0, 104, 104, 0, 143, 1, 1, 93, 93, 0, 118, 11, 0, 29, 29, 1, 64,
64, 1, 146, 4, 1, 137, 30, 1, 229, 29, 2, 70, 70, 1, 44, 44, 1, 49,
49, 1, 117, 10, 0, 152, 10, 0, 130, 23, 1, 26, 26, 1, 110, 3, 1,
158, 16, 0, 124, 17, 0, 206, 6, 0, 141, 34, 1, 92, 92, 0, 32, 32,
1, 27, 27, 0, 58, 58, 0, 162, 20, 0, 13, 13, 0, 187, 45, 1, 223,
23, 0, 43, 43, 0, 48, 48, 0, 176, 34, 0, 99, 99, 0, 149, 7, 1, 231,
31, 1, 180, 38, 0, 18, 18, 0, 55, 55, 0, 169, 27, 2, 164, 22, 1,
208, 8, 1, 116, 9, 0, 87, 87, 0, 15, 15
])
collation = Collation()
_, child_lcp_intervals = collation.get_lcp_intervals(lcp=lcp_array)
self.assertEqual([(5, 7), (8, 10)], child_lcp_intervals[5])
self.assertEqual([(513, 515), (516, 518), (519, 521), (522, 524),
(525, 527)], child_lcp_intervals[513])
def test_lcp_child_intervals_darwin(self):
lcp_array = array('i', [0, 0, 0, 96, 96, 0, 151, 9, 1, 105, 105, 0, 83, 83, 0, 95, 95, 0, 39, 39, 0, 24, 24, 0, 108, 1, 0, 232, 32, 0, 181, 39, 0, 185, 43, 1, 33, 33, 0, 159, 17, 0, 160, 18, 0, 106, 106, 0, 60, 60, 0, 171, 29, 1, 215, 15, 1, 122, 15, 1, 57, 57, 1, 153, 11, 1, 165, 23, 0, 9, 9, 1, 170, 28, 0, 214, 14, 0, 62, 62, 1, 191, 49, 0, 61, 61, 0, 148, 6, 1, 8, 8, 0, 19, 19, 0, 123, 16, 0, 75, 75, 1, 90, 90, 1, 28, 28, 0, 167, 25, 1, 112, 5, 1, 132, 25, 0, 50, 50, 0, 31, 31, 0, 77, 77, 0, 97, 97, 0, 6, 6, 0, 38, 38, 0, 63, 63, 0, 30, 30, 0, 80, 80, 0, 154, 12, 0, 145, 3, 0, 129, 22, 3, 67, 67, 0, 88, 88, 0, 45, 45, 0, 217, 17, 1, 22, 22, 0, 166, 24, 0, 25, 25, 0, 201, 1, 0, 155, 13, 1, 120, 13, 0, 175, 33, 0, 195, 53, 0, 135, 28, 0, 10, 10, 0, 147, 5, 0, 138, 31, 0, 161, 19, 1, 73, 73, 0, 198, 1, 0, 86, 86, 0, 74, 74, 1, 111, 4, 0, 210, 10, 0, 84, 84, 0, 42, 42, 0, 199, 2, 0, 119, 12, 0, 46, 46, 1, 202, 2, 0, 71, 71, 0, 40, 40, 0, 142, 0, 0, 52, 52, 0, 168, 26, 2, 113, 6, 1, 163, 21, 0, 133, 26, 0, 3, 3, 0, 186, 44, 1, 101, 101, 0, 193, 51, 2, 227, 27, 0, 107, 1, 37, 37, 1, 140, 33, 0, 1, 205, 5, 0, 47, 47, 0, 127, 20, 1, 65, 65, 0, 230, 30, 0, 41, 41, 0, 91, 91, 0, 1, 1, 0, 200, 3, 0, 156, 14, 0, 0, 76, 76, 0, 109, 2, 1, 182, 40, 0, 68, 68, 1, 14, 14, 0, 126, 19, 0, 34, 34, 1, 192, 50, 1, 85, 85, 1, 128, 21, 2, 66, 66, 1, 183, 41, 1, 220, 20, 1, 5, 5, 1, 212, 12, 2, 174, 32, 2, 226, 26, 1, 59, 59, 0, 16, 16, 0, 218, 18, 0, 23, 23, 1, 11, 11, 0, 36, 36, 1, 178, 36, 0, 51, 51, 0, 213, 13, 1, 190, 48, 0, 2, 2, 1, 222, 22, 1, 188, 46, 0, 78, 78, 0, 53, 53, 0, 197, 0, 0, 136, 29, 1, 219, 19, 1, 12, 12, 0, 114, 7, 0, 89, 89, 0, 172, 30, 2, 216, 16, 0, 21, 21, 0, 209, 9, 0, 81, 81, 0, 102, 102, 0, 134, 27, 0, 98, 98, 0, 131, 24, 0, 4, 4, 0, 35, 35, 0, 179, 37, 0, 224, 24, 0, 82, 82, 0, 72, 72, 0, 139, 32, 0, 125, 18, 0, 103, 103, 0, 121, 14, 0, 189, 47, 0, 184, 42, 0, 7, 7, 1, 17, 17, 0, 207, 7, 0, 221, 21, 0, 20, 20, 0, 196, 54, 0, 79, 79, 1, 204, 4, 1, 144, 2, 2, 94, 94, 1, 56, 56, 0, 211, 11, 1, 194, 52, 3, 228, 28, 1, 157, 15, 1, 69, 69, 1, 54, 54, 1, 115, 8, 1, 173, 31, 1, 225, 25, 1, 177, 35, 1, 100, 100, 0, 203, 3, 0, 150, 8, 0, 104, 104, 0, 143, 1, 1, 93, 93, 0, 118, 11, 0, 29, 29, 1, 64, 64, 1, 146, 4, 1, 137, 30, 1, 229, 29, 2, 70, 70, 1, 44, 44, 1, 49, 49, 1, 117, 10, 0, 152, 10, 0, 130, 23, 1, 26, 26, 1, 110, 3, 1, 158, 16, 0, 124, 17, 0, 206, 6, 0, 141, 34, 1, 92, 92, 0, 32, 32, 1, 27, 27, 0, 58, 58, 0, 162, 20, 0, 13, 13, 0, 187, 45, 1, 223, 23, 0, 43, 43, 0, 48, 48, 0, 176, 34, 0, 99, 99, 0, 149, 7, 1, 231, 31, 1, 180, 38, 0, 18, 18, 0, 55, 55, 0, 169, 27, 2, 164, 22, 1, 208, 8, 1, 116, 9, 0, 87, 87, 0, 15, 15])
collation = Collation()
_, child_lcp_intervals = collation.get_lcp_intervals(lcp=lcp_array)
self.assertEqual([(5, 7), (8, 10)], child_lcp_intervals[5])
self.assertEqual([(513, 515),(516, 518),(519, 521),(522, 524),(525,527)], child_lcp_intervals[513])
