def test_random_aaaa(self):
lengths = [1, 2, 3, 10, 100, 1000]
for length in lengths:
text = ''.join('a' for _ in range(length))
self.assertTupleEqual(
suffix_array(text), naive_suffix_array(text)
)
def test_random_aaaa(self):
lengths = [1, 2, 3, 10, 100, 1000]
for length in lengths:
text = ''.join('a' for _ in range(length))
sa = suffix_array(text)
correct_lcp = tuple(i for i in range(len(text)))
self.assertTupleEqual(
lcp_array(text, sa), correct_lcp
)
def test_random_strings(self):
alphabet = string.printable
cnt = 200
max_length = 1000
for t in range(cnt):
length = random.randint(1, max_length)
text = ''.join(random.choice(alphabet) for _ in range(length))
self.assertTupleEqual(
suffix_array(text), naive_suffix_array(text)
)
def test_random_strings(self):
alphabet = string.printable
cnt = 200
max_length = 1000
for t in range(cnt):
length = random.randint(1, max_length)
text = ''.join(random.choice(alphabet) for _ in range(length))
sa = suffix_array(text)
lcpa = lcp_array(text, sa)
for i in range(1, len(lcpa)):
self.assertEqual(
text[sa[i]:sa[i] + lcpa[i]],
text[sa[i-1]:sa[i-1] + lcpa[i]],
)
if sa[i] + lcpa[i] + 1 < len(text) and sa[i - 1] + lcpa[i] + 1 < len(text):
self.assertNotEqual(
text[sa[i]:sa[i] + lcpa[i] + 1],
text[sa[i - 1]:sa[i - 1] + lcpa[i] + 1],
)
def test_keep_tree(self):
lcp = []
lb = []
rb = []
def action(node):
lcp.append(node.lcp)
lb.append(node.lb)
rb.append(node.rb)
correct_lcp = [3, 2, 1, 4, 1, 0]
correct_lb = [0, 2, 0, 6, 6, 0]
correct_rb = [2, 4, 4, 8, 9, 9]
text = 'ctaataatg'
sa = suffix_array(text)
lcpa = lcp_array(text, sa)
root = bottom_up_lcp_interval_tree_traverse(lcpa, action, keep_tree=True)
self.assertListEqual(lcp, correct_lcp)
self.assertListEqual(lb, correct_lb)
self.assertListEqual(rb, correct_rb)
self.assertEqual(root.lcp, 0)
self.assertEqual(root.lb, 0)
self.assertEqual(root.rb, 9)
node = root.get(0)
self.assertEqual(node.lcp, 1)
self.assertEqual(node.lb, 0)
self.assertEqual(node.rb, 4)
node2 = node.get(0)
self.assertEqual(node2.lcp, 3)
self.assertEqual(node2.lb, 0)
self.assertEqual(node2.rb, 2)
node2 = node.get(1)
self.assertEqual(node2.lcp, 2)
node2 = root.get(1)
self.assertEqual(node2.lcp, 1)
node2 = root.get(1).get(0)
self.assertEqual(node2.lcp, 4)
def test_traverse(self):
lcp = []
lb = []
rb = []
def action(node):
lcp.append(node.lcp)
lb.append(node.lb)
rb.append(node.rb)
text = 'ctaataatg'
sa = suffix_array(text)
lcpa = lcp_array(text, sa)
bottom_up_lcp_interval_tree_traverse(lcpa, action)
correct_lcp = [3, 2, 1, 4, 1, 0]
correct_lb = [0, 2, 0, 6, 6, 0]
correct_rb = [2, 4, 4, 8, 9, 9]
self.assertListEqual(lcp, correct_lcp)
self.assertListEqual(lb, correct_lb)
self.assertListEqual(rb, correct_rb)
def test_traverse(self):
lcp = []
lb = []
rb = []
def action(node, *_):
lcp.append(node.lcp)
lb.append(node.lb)
rb.append(node.rb)
text = 'ctaataatg'
sa = suffix_array(text)
lcpa = lcp_array(text, sa)
tree = LCPConceptualIntervalTree(lcpa)
tree.dfs(pre_action=action)
correct_lcp = [0, 1, 3, 2, 1, 4]
correct_lb = [0, 0, 0, 2, 6, 6]
correct_rb = [9, 4, 2, 4, 9, 8]
self.assertListEqual(lcp, correct_lcp)
self.assertListEqual(lb, correct_lb)
self.assertListEqual(rb, correct_rb)
def test_lcp_array(self):
text = 'ctaataatg'
sa = suffix_array(text)
self.assertTupleEqual(lcp_array(text, sa), (0, 3, 1, 2, 0, 0, 0, 4, 1))
def test_empty_string(self):
self.assertTupleEqual(
suffix_array(''), tuple()
)
def test_suffix_array2(self):
text = 'imimmmisismisissiipi'
self.assertTupleEqual(
suffix_array(text), (19, 16, 0, 2, 17, 6, 11, 8, 13, 1, 5, 10, 4, 3, 18, 15, 7, 12, 9, 14)
)
def test_suffix_array(self):
text = 'ctaataatg'
self.assertTupleEqual(suffix_array(text), (2, 5, 3, 6, 0, 8, 1, 4, 7))
def sa_preprocess(text):
sa = suffix_array(text)
lcp = lcp_array(text, sa)
lcptree = LCPConceptualIntervalTree(lcp, include_singletons=True)
return text, sa, lcptree