def test_all_suffix_array(self):
N, A = 12, ['a', 'b']
for n in range(2, N + 1):
for t in itertools.product(A, repeat = n):
t = '#' + ''.join(t)
reference = suffix_array.naive(t, n)
self.check_suffix_array(t, n, reference)
def check_maximum_suffix(self, t, n, reference):
for algorithm in MAXIMUM_SUFFIX_ALGORITHMS:
self.assertEqual(
algorithm(t, n),
reference,
'Algorithm: {0}'.format(algorithm.__name__))
self.assertEqual(
suffix_array.naive(t, n)[-1],
reference[0],
'Maximum suffix from suffix array')
def check_no_match(self, t, w, n, m):
for algorithm in EXACT_STRING_MATCHING_ALGORITHMS:
self.assertFalse(
list(algorithm(t, w, n, m)),
'Algorithm {}, text {}, pattern {}'.format(
algorithm.__name__, t, w))
self.assertFalse(
list(suffix_tree.contains(suffix_tree.naive(t, n), t, w, n, m)),
'Suffix tree, text {}, pattern {}'.format(t, w))
self.assertFalse(
list(suffix_array.contains(suffix_array.naive(t, n), t, w, n, m)),
'Suffix array, text {}, pattern {}'.format(t, w))
def check_get_all_exact_matches(self, t, w, n, m, reference):
for algorithm in EXACT_STRING_MATCHING_ALGORITHMS:
self.assertEqual(
list(algorithm(t, w, n, m)), reference,
'Algorithm {}, text {}, pattern {}'.format(
algorithm.__name__, t, w))
self.assertEqual(
list(suffix_tree.contains(suffix_tree.naive(t, n), t, w, n, m)),
reference, 'Suffix tree, text {}, pattern {}'.format(t, w))
self.assertEqual(
list(suffix_array.contains(suffix_array.naive(t, n), t, w, n, m)),
reference, 'Suffix array, text {}, pattern {}'.format(t, w))
def test_random_suffix_array(self):
T, n, A = 100, 500, ['a', 'b']
for _ in range(T):
t = rand.random_word(n, A)
reference = suffix_array.naive(t, n)
self.check_suffix_array(t, n, reference)
def check_burrows_wheeler(self, t, n, reference):
self.assertEqual(burrows_wheeler.transform_from_suffix_array(
suffix_array.naive(t, n), t, n), reference)
import itertools
import os
import unittest
import parameterized
from generator import rand
from string_indexing import suffix_array
from lyndon import maximum_suffix
MAXIMUM_SUFFIX_ALGORITHMS = [
['from prefix suffix', maximum_suffix.from_prefix_suffix],
['constant space', maximum_suffix.constant_space],
[
'from suffix array', lambda t, n: maximum_suffix.from_suffix_array(
suffix_array.naive(t, n), t, n)
],
]
class TestMaximumSuffix(unittest.TestCase):
run_large = unittest.skipUnless(os.environ.get('LARGE', False),
'Skip test in small runs')
def check_maximum_suffix(self, t, n, reference, algorithm):
self.assertEqual(algorithm(t, n), reference,
'Algorithm: {}'.format(algorithm.__name__))
@parameterized.parameterized.expand(MAXIMUM_SUFFIX_ALGORITHMS)
def test_maximum_suffix(self, _, algorithm):
self.check_maximum_suffix('#abaaba', 6, (2, 3), algorithm)