def test_lower_mod_prod(self):
"""
If a substring does not exist, check if substrings of that substring exist.
A simple utility function to compute \prod_{j=jmin}^{jmax} f_tree(w[j:j+l])
"""
string = 'aaaa' + 'bc' + 'aaaa' + 'cd' + 'aaaa' + 'de' + 'aaaa'
tree = TARZAN.SuffixTree(string, method='McCreight')
tree.root._annotate_nodes()
prob = TARZAN._lower_mod_prod(tree, 'bcde', 0, 2, 2)
self.assertEqual(prob, 1)
def test_SymbolProbability(self):
"""
If the substring does not exist and not all substrings of the substring
exist then we compute product of the probabilities of each symbol
"""
string = 'abababa' + 'c' + 'abababa' + 'd' + 'abababa'
tree = TARZAN.SuffixTree(string, method='McCreight')
tree.root._annotate_nodes()
prob = TARZAN._symbol_prob(tree, string, 'cd')
self.assertTrue(np.allclose(prob, 1 / (len(string)**2)))
prob = TARZAN._symbol_prob(tree, string, 'bc')
self.assertTrue(np.allclose(prob, 9 / (len(string)**2)))
prob = TARZAN._symbol_prob(tree, string, 'ab')
self.assertTrue(np.allclose(prob, 108 / (len(string)**2)))
def test_tree_LargeExample(self):
"""
Test suffix tree construction and find function on a very large example.
"""
string = ''.join([choice(ascii_lowercase) for _ in range(1000000)])
tree = TARZAN.SuffixTree(string, method='McCreight')
l = tree.find(string[6783:6789])
self.assertTrue(6783 in l)
def test_build_tree_BruteForce(self):
"""
Test Brute Force algorithm implementation
"""
string = 'banana'
tree = TARZAN.SuffixTree(string, method='Brute')
self.assertEqual(tree.find('an'), [1, 3])
self.assertEqual(tree.find('a'), [1, 3, 5])
self.assertEqual(tree.find('ab'), [])
self.assertEqual(tree.find('nan'), [2])
def test_compute_expectation(self):
"""
Test simple Tarzan example by finding in predefined string using method==None
"""
R = 'abcbabcbabcbabcba'
X = 'abccba'
Rtree = TARZAN.SuffixTree(R, method='McCreight')
Rtree.root._annotate_nodes()
E1 = TARZAN.compute_expectation('abc', R, X, Rtree)
E2 = TARZAN.compute_expectation('bcc', R, X, Rtree)
self.assertEqual(E1, (len(X) - 3 + 1) / (len(R) - 3 + 1) * 4)
self.assertEqual(E2, (len(X) - 3 + 1) * ((8 * 4 * 4) / (17**3)))
score = TARZAN.TARZAN(R, X, 3, method=None)
self.assertEqual(abs(E1 - 1), score[1])
self.assertEqual(abs(E2 - 1), score[2])
def test_build_tree_McCreight(self):
"""
Test McCreight algorithm implementation
"""
string = 'banana'
tree = TARZAN.SuffixTree(string, method='McCreight')
self.assertEqual(tree.find('an'), [1, 3])
self.assertEqual(tree.find('a'), [1, 3, 5])
self.assertEqual(tree.find('ab'), [])
self.assertEqual(tree.find('nan'), [2])
def test_tree_annotate(self):
"""
Check the annotate node function finds the frequency of each word correctly.
"""
string = 'banana'
tree = TARZAN.SuffixTree(string, method='McCreight')
tree.root._annotate_nodes()
node = tree.find('b', list_all=False, index=False)
self.assertEqual(node.frequency, 1)
node = tree.find('a', list_all=False, index=False)
self.assertEqual(node.frequency, 3)
node = tree.find('n', list_all=False, index=False)
self.assertEqual(node.frequency, 2)
node = tree.find('an', list_all=False, index=False)
self.assertEqual(node.frequency, 2)
node = tree.find('ana', list_all=False, index=False)
self.assertEqual(node.frequency, 2)
node = tree.find('ban', list_all=False, index=False)
self.assertEqual(node.frequency, 1)
def test_tree_find(self):
"""
Test all variants of SuffixTree find function
"""
string = 'bananahanana'
tree = TARZAN.SuffixTree(string, method='McCreight')
# returns a list of indicies
l = tree.find('an', list_all=True, index=True)
self.assertEqual(l.sort(), [1, 3, 7, 9].sort())
# returns a list of nodes
l = tree.find('an', list_all=True, index=False)
self.assertEqual(len(l), 4)
self.assertTrue(isinstance(l[0], TARZAN._Node))
# returns a bool
l = tree.find('an', list_all=False, index=True)
self.assertTrue(l)
# returns a node
l = tree.find('an', list_all=False, index=False)
self.assertTrue(isinstance(l, TARZAN._Node))