def test_edges_for_ataaatg(self):
words = [
'ATAAATG',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'ATAAATG$',
], tree._words)
expected_edges = [
'A',
'T',
'G$',
'$',
'A',
'T',
'ATG$',
'TG$',
'AAATG$',
'G$',
'AAATG$',
'G$',
]
self.assert_edge_strings(expected_edges, tree)
def test_node_depth_in_tree_with_one_word(self):
words = [
'word',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'word$',
], tree._words)
self.assertEqual(6, len(tree._nodes))
self.assertEqual('', tree.node_substring(0))
self.assertEqual(0, tree.node_depth(0))
self.assertEqual('word$', tree.node_substring(1))
self.assertEqual(4, tree.node_depth(1))
self.assertEqual('ord$', tree.node_substring(2))
self.assertEqual(3, tree.node_depth(2))
self.assertEqual('rd$', tree.node_substring(3))
self.assertEqual(2, tree.node_depth(3))
self.assertEqual('d$', tree.node_substring(4))
self.assertEqual(1, tree.node_depth(4))
self.assertEqual('$', tree.node_substring(5))
self.assertEqual(0, tree.node_depth(5))
def test_node_substring_in_tree_with_two_words(self):
words = [
'panama',
'banana',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'panama$0',
'banana$1',
], tree._words)
self.assertEqual(18, len(tree._nodes))
self.assertEqual('', tree.node_substring(0))
self.assertEqual('panama$0', tree.node_substring(1))
self.assertEqual('anama$0', tree.node_substring(2))
self.assertEqual('nama$0', tree.node_substring(3))
self.assertEqual('a', tree.node_substring(4))
self.assertEqual('ama$0', tree.node_substring(5))
self.assertEqual('ma$0', tree.node_substring(6))
self.assertEqual('a$0', tree.node_substring(7))
self.assertEqual('$0', tree.node_substring(8))
self.assertEqual('banana$1', tree.node_substring(9))
self.assertEqual('ana', tree.node_substring(10))
self.assertEqual('anana$1', tree.node_substring(11))
self.assertEqual('na', tree.node_substring(12))
self.assertEqual('nana$1', tree.node_substring(13))
self.assertEqual('ana$1', tree.node_substring(14))
self.assertEqual('na$1', tree.node_substring(15))
self.assertEqual('a$1', tree.node_substring(16))
self.assertEqual('$1', tree.node_substring(17))
def test_edge_substring_in_tree_with_two_words(self):
words = [
'panama',
'banana',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'panama$0',
'banana$1',
], tree._words)
self.assertEqual(17, len(tree._edges))
edge = tree._edges[(0, 1)]
self.assertEqual('panama$0', tree.edge_substring(edge))
edge = tree._edges[(0, 4)]
self.assertEqual('a', tree.edge_substring(edge))
edge = tree._edges[(0, 6)]
self.assertEqual('ma$0', tree.edge_substring(edge))
edge = tree._edges[(0, 8)]
self.assertEqual('$0', tree.edge_substring(edge))
edge = tree._edges[(0, 9)]
self.assertEqual('banana$1', tree.edge_substring(edge))
edge = tree._edges[(0, 12)]
self.assertEqual('na', tree.edge_substring(edge))
edge = tree._edges[(0, 17)]
self.assertEqual('$1', tree.edge_substring(edge))
edge = tree._edges[(4, 5)]
self.assertEqual('ma$0', tree.edge_substring(edge))
edge = tree._edges[(4, 7)]
self.assertEqual('$0', tree.edge_substring(edge))
edge = tree._edges[(4, 10)]
self.assertEqual('na', tree.edge_substring(edge))
edge = tree._edges[(4, 16)]
self.assertEqual('$1', tree.edge_substring(edge))
edge = tree._edges[(12, 3)]
self.assertEqual('ma$0', tree.edge_substring(edge))
edge = tree._edges[(12, 13)]
self.assertEqual('na$1', tree.edge_substring(edge))
edge = tree._edges[(12, 15)]
self.assertEqual('$1', tree.edge_substring(edge))
edge = tree._edges[(10, 2)]
self.assertEqual('ma$0', tree.edge_substring(edge))
edge = tree._edges[(10, 11)]
self.assertEqual('na$1', tree.edge_substring(edge))
edge = tree._edges[(10, 14)]
self.assertEqual('$1', tree.edge_substring(edge))
def test_edges_for_aca(self):
words = [
'ACA',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'ACA$',
], tree._words)
expected_edges = [
'CA$',
'A',
'$',
'CA$',
'$',
]
self.assert_edge_strings(expected_edges, tree)
def test_edge_substring_in_tree_with_one_word(self):
words = [
'word',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'word$',
], tree._words)
self.assertEqual(5, len(tree._edges))
edge = tree._edges[(0, 1)]
self.assertEqual('word$', tree.edge_substring(edge))
edge = tree._edges[(0, 2)]
self.assertEqual('ord$', tree.edge_substring(edge))
edge = tree._edges[(0, 3)]
self.assertEqual('rd$', tree.edge_substring(edge))
edge = tree._edges[(0, 4)]
self.assertEqual('d$', tree.edge_substring(edge))
edge = tree._edges[(0, 5)]
self.assertEqual('$', tree.edge_substring(edge))
def test_constructor_with_two_words(self):
words = [
'panama',
'banana',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'panama$0',
'banana$1',
], tree._words)
expected_nodes = []
expected_edges = []
self.assertEqual(18, len(tree._nodes))
self.assertEqual(17, len(tree._edges))
self.assertEqual(len(tree._nodes) - 1, len(tree._edges))
self.assertEqual(-1, tree._nodes[0].parent)
self.assertEqual([
1,
4,
6,
8,
9,
12,
17,
], tree._nodes[0].children)
self.assertEqual(set([
0,
1,
]), tree._nodes[0].words)
expected_nodes.append(0)
self.assertEqual(0, tree._nodes[1].parent)
self.assertEqual([], tree._nodes[1].children)
self.assertEqual(set([
0,
]), tree._nodes[1].words)
expected_nodes.append(1)
self.assertEqual(0, tree._nodes[4].parent)
self.assertEqual([
5,
7,
10,
16,
], tree._nodes[4].children)
self.assertEqual(set([
0,
1,
]), tree._nodes[4].words)
expected_nodes.append(4)
self.assertEqual(0, tree._nodes[6].parent)
self.assertEqual([], tree._nodes[6].children)
self.assertEqual(set([
0,
]), tree._nodes[6].words)
expected_nodes.append(6)
self.assertEqual(0, tree._nodes[8].parent)
self.assertEqual([], tree._nodes[8].children)
self.assertEqual(set([
0,
]), tree._nodes[8].words)
expected_nodes.append(8)
self.assertEqual(0, tree._nodes[9].parent)
self.assertEqual([], tree._nodes[9].children)
self.assertEqual(set([
1,
]), tree._nodes[9].words)
expected_nodes.append(9)
self.assertEqual(0, tree._nodes[12].parent)
self.assertEqual([
3,
13,
15,
], tree._nodes[12].children)
self.assertEqual(set([
0,
1,
]), tree._nodes[12].words)
expected_nodes.append(12)
self.assertEqual(0, tree._nodes[17].parent)
self.assertEqual([], tree._nodes[17].children)
self.assertEqual(set([
1,
]), tree._nodes[17].words)
expected_nodes.append(17)
self.assertEqual(4, tree._nodes[5].parent)
self.assertEqual([], tree._nodes[5].children)
self.assertEqual(set([
0,
]), tree._nodes[5].words)
expected_nodes.append(5)
self.assertEqual(4, tree._nodes[7].parent)
self.assertEqual([], tree._nodes[7].children)
self.assertEqual(set([
0,
]), tree._nodes[7].words)
expected_nodes.append(7)
self.assertEqual(4, tree._nodes[10].parent)
self.assertEqual([
2,
11,
14,
], tree._nodes[10].children)
self.assertEqual(set([
0,
1,
]), tree._nodes[10].words)
expected_nodes.append(10)
self.assertEqual(4, tree._nodes[16].parent)
self.assertEqual([], tree._nodes[16].children)
self.assertEqual(set([
1,
]), tree._nodes[16].words)
expected_nodes.append(16)
self.assertEqual(12, tree._nodes[3].parent)
self.assertEqual([], tree._nodes[3].children)
self.assertEqual(set([
0,
]), tree._nodes[3].words)
expected_nodes.append(3)
self.assertEqual(12, tree._nodes[13].parent)
self.assertEqual([], tree._nodes[13].children)
self.assertEqual(set([
1,
]), tree._nodes[13].words)
expected_nodes.append(13)
self.assertEqual(12, tree._nodes[15].parent)
self.assertEqual([], tree._nodes[15].children)
self.assertEqual(set([
1,
]), tree._nodes[15].words)
expected_nodes.append(15)
self.assertEqual(10, tree._nodes[2].parent)
self.assertEqual([], tree._nodes[2].children)
self.assertEqual(set([
0,
]), tree._nodes[2].words)
expected_nodes.append(2)
self.assertEqual(10, tree._nodes[11].parent)
self.assertEqual([], tree._nodes[11].children)
self.assertEqual(set([
1,
]), tree._nodes[11].words)
expected_nodes.append(11)
self.assertEqual(10, tree._nodes[14].parent)
self.assertEqual([], tree._nodes[14].children)
self.assertEqual(set([
1,
]), tree._nodes[14].words)
expected_nodes.append(14)
self.assert_items(expected_nodes, list(range(len(tree._nodes))))
edge = tree._edges[(0, 1)]
self.assertEqual(0, edge._word_index)
self.assertEqual(0, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('panama$0', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 4)]
self.assertEqual(0, edge._word_index)
self.assertEqual(1, edge._start_index)
self.assertEqual(2, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('a', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 6)]
self.assertEqual(0, edge._word_index)
self.assertEqual(4, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('ma$0', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 8)]
self.assertEqual(0, edge._word_index)
self.assertEqual(6, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('$0', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 9)]
self.assertEqual(1, edge._word_index)
self.assertEqual(0, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('banana$1', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 12)]
self.assertEqual(0, edge._word_index)
self.assertEqual(2, edge._start_index)
self.assertEqual(4, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('na', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 17)]
self.assertEqual(1, edge._word_index)
self.assertEqual(6, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('$1', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(4, 5)]
self.assertEqual(0, edge._word_index)
self.assertEqual(4, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('ma$0', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(4, 7)]
self.assertEqual(0, edge._word_index)
self.assertEqual(6, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('$0', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(4, 10)]
self.assertEqual(0, edge._word_index)
self.assertEqual(2, edge._start_index)
self.assertEqual(4, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('na', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(4, 16)]
self.assertEqual(1, edge._word_index)
self.assertEqual(6, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('$1', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(12, 3)]
self.assertEqual(0, edge._word_index)
self.assertEqual(4, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('ma$0', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(12, 13)]
self.assertEqual(1, edge._word_index)
self.assertEqual(4, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('na$1', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(12, 15)]
self.assertEqual(1, edge._word_index)
self.assertEqual(6, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('$1', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(10, 2)]
self.assertEqual(0, edge._word_index)
self.assertEqual(4, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('ma$0', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(10, 11)]
self.assertEqual(1, edge._word_index)
self.assertEqual(4, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('na$1', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(10, 14)]
self.assertEqual(1, edge._word_index)
self.assertEqual(6, edge._start_index)
self.assertEqual(8, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('$1', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
self.assert_items(expected_edges, tree._edges.values())
def test_constructor_with_one_word(self):
words = [
'word',
]
tree = generalized_suffix_tree.GeneralizedSuffixTree(words)
self.assertEqual([
'word$',
], tree._words)
expected_nodes = []
expected_edges = []
self.assertEqual(6, len(tree._nodes))
self.assertEqual(5, len(tree._edges))
self.assertEqual(len(tree._nodes) - 1, len(tree._edges))
self.assertEqual(-1, tree._nodes[0].parent)
self.assertEqual([
1,
2,
3,
4,
5,
], tree._nodes[0].children)
self.assertEqual(set([
0,
]), tree._nodes[0].words)
expected_nodes.append(0)
self.assertEqual(0, tree._nodes[1].parent)
self.assertEqual([], tree._nodes[1].children)
self.assertEqual(set([
0,
]), tree._nodes[1].words)
expected_nodes.append(1)
self.assertEqual(0, tree._nodes[2].parent)
self.assertEqual([], tree._nodes[2].children)
self.assertEqual(set([
0,
]), tree._nodes[2].words)
expected_nodes.append(2)
self.assertEqual(0, tree._nodes[3].parent)
self.assertEqual([], tree._nodes[3].children)
self.assertEqual(set([
0,
]), tree._nodes[3].words)
expected_nodes.append(3)
self.assertEqual(0, tree._nodes[4].parent)
self.assertEqual([], tree._nodes[4].children)
self.assertEqual(set([
0,
]), tree._nodes[4].words)
expected_nodes.append(4)
self.assertEqual(0, tree._nodes[5].parent)
self.assertEqual([], tree._nodes[5].children)
self.assertEqual(set([
0,
]), tree._nodes[5].words)
expected_nodes.append(5)
self.assert_items(expected_nodes, list(range(len(tree._nodes))))
edge = tree._edges[(0, 1)]
self.assertEqual(0, edge._word_index)
self.assertEqual(0, edge._start_index)
self.assertEqual(5, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('word$', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 2)]
self.assertEqual(0, edge._word_index)
self.assertEqual(1, edge._start_index)
self.assertEqual(5, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('ord$', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 3)]
self.assertEqual(0, edge._word_index)
self.assertEqual(2, edge._start_index)
self.assertEqual(5, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('rd$', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 4)]
self.assertEqual(0, edge._word_index)
self.assertEqual(3, edge._start_index)
self.assertEqual(5, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('d$', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
edge = tree._edges[(0, 5)]
self.assertEqual(0, edge._word_index)
self.assertEqual(4, edge._start_index)
self.assertEqual(5, edge._stop_index)
word = tree._words[edge._word_index]
self.assertEqual('$', word[edge._start_index:edge._stop_index])
expected_edges.append(edge)
self.assert_items(expected_edges, tree._edges.values())