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#!/usr/bin/env python
"""tests for Trie and compressed Trie class."""
__author__ = "Jens Reeder"
__copyright__ = "Copyright 2009, the PyCogent Project"
__credits__ = ["Jens Reeder"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
__status__ = "Prototype"
from cogent.util.unit_test import TestCase, main
from cogent.util.trie import Trie, Compressed_Trie, build_prefix_map, build_trie, \
_build_prefix_map
class TrieTests(TestCase):
def setUp(self):
self.data = dict({"0": "ab", "1":"abababa", "2":"abab",
"3":"baba", "4":"ababaa","5":"a", "6":"abababa",
"7":"bab", "8":"babba"})
def test_init(self):
"""Trie init should create an empty trie."""
t = Trie()
self.assertEqual(t.root.labels, [])
self.assertEqual(t.root.children, {})
def test_insert_find(self):
"""An added key should be found by find."""
data = self.data
t = Trie()
for (label, seq) in data.iteritems():
t.insert(seq, label)
for (label, seq) in data.iteritems():
self.assertEqual(label in t.find(seq), True)
self.assertEqual(t.find("cacgchagc"), [])
self.assertEqual(t.find("abababa"), ["1","6"])
def test_insert_unique(self):
"""insert_unique should insert only unique words."""
data = self.data
t = Trie()
for (label, seq) in data.iteritems():
t._insert_unique(seq, label)
self.assertEqual(t.find("ab"), [])
self.assertEqual(t.find("cacgchagc"), [])
self.assertEqual(t.find("abababa"), ["1"])
def test_build_prefix_map(self):
"""prefix_map should map prefix strings."""
self.assertEqual(dict(_build_prefix_map(self.data.iteritems())),
{'1': ['0', '2', '5', '6'],
'8': [],
'3': ['7'],
'4': []})
class Compressed_Trie_Tests(TestCase):
def setUp(self):
self.data = dict({"0": "ab", "1":"abababa", "2":"abab",
"3":"baba", "4":"ababaa","5":"a", "6":"abababa",
"7":"bab", "8":"babba"})
self.trie = build_trie(self.data.iteritems())
def test_init(self):
"""Trie init should create an empty trie."""
t = Compressed_Trie()
self.assertEqual(t.root.labels, [])
self.assertEqual(t.root.children, {})
self.assertEqual(t.root.key, "")
def test_non_zero(self):
"""__non_zero__ should cehck for any data in the trie."""
t = Compressed_Trie()
self.assertEqual(t.__nonzero__(), False)
self.assertEqual(self.trie.__nonzero__(), True)
def test_len(self):
"""__len__ should return the number of seqs in the trie."""
self.assertEqual(len(self.trie), 9)
t = Compressed_Trie()
self.assertEqual(len(t), 0)
def test_size(self):
"""size should return the number of nodes in the trie."""
self.assertEqual(self.trie.size(), 10)
#empty trie contins only root node
t = Compressed_Trie()
self.assertEqual(size(t), 1)
def test_to_string(self):
"""_to_string should create a string representation."""
string_rep = """
key
{
\tkey a['5']
\t{
\t\tkey b['0']
\t\t{
\t\t\tkey ab['2']
\t\t\t{
\t\t\t\tkey a
\t\t\t\t{
\t\t\t\t\tkey a['4']
\t\t\t\t}
\t\t\t\t{
\t\t\t\t\tkey ba['1', '6']
\t\t\t\t}
\t\t\t}
\t\t}
\t}
}
{
\tkey bab['7']
\t{
\t\tkey a['3']
\t}
\t{
\t\tkey ba['8']
\t}
}
"""
self.assertEqual(str(self.trie), string_rep)
def test_insert_find(self):
"""An added key should be found by find."""
data = self.data
t = Compressed_Trie()
for (label, seq) in data.iteritems():
t.insert(seq, label)
for (label, seq) in data.iteritems():
self.assertEqual(label in t.find(seq), True)
self.assertEqual(t.find("abababa"), ["1","6"])
self.assertEqual(t.find("cacgchagc"), [])
def test_prefixMap(self):
"""prefix_map (Compressed_Trie) should map prefix strings."""
self.assertEqual(self.trie.prefixMap(),
{'1': ['6', '2', '0', '5'],
'8': ['7'],
'3': [],
'4': []})
def test_init(self):
"""Trie init should create an empty trie."""
t = Trie()
self.assertEqual(t.root.labels, [])
self.assertEqual(t.root.children, {})
def test_insert_find(self):
"""An added key should be found by find."""
data = self.data
t = Trie()
for (label, seq) in data.iteritems():
t.insert(seq, label)
for (label, seq) in data.iteritems():
self.assertEqual(label in t.find(seq), True)
self.assertEqual(t.find("cacgchagc"), [])
self.assertEqual(t.find("abababa"), ["1","6"])
def test_insert_unique(self):
"""insert_unique should insert only unique words."""
data = self.data
t = Trie()
for (label, seq) in data.iteritems():
t._insert_unique(seq, label)
self.assertEqual(t.find("ab"), [])
self.assertEqual(t.find("cacgchagc"), [])
self.assertEqual(t.find("abababa"), ["1"])
def test_build_prefix_map(self):
"""prefix_map should map prefix strings."""
self.assertEqual(dict(_build_prefix_map(self.data.iteritems())),
{'1': ['0', '2', '5', '6'],
'8': [],
'3': ['7'],
'4': []})
def test_build_trie(self):
"""Build_trie should build trie from seqs."""
t = build_trie(self.data.iteritems(), Trie)
self.assertTrue(isinstance(t, Trie))
for (label, seq) in self.data.iteritems():
self.assertContains(t.find(seq), label)
self.assertEqual(t.find(""), [])
self.assertEqual(t.find("ccc"), [])
class Compressed_Trie_Tests(TestCase):
def setUp(self):
self.data = dict({"0": "ab", "1":"abababa", "2":"abab",
"3":"baba", "4":"ababaa","5":"a", "6":"abababa",
"7":"bab", "8":"babba"})
self.trie = build_trie(self.data.iteritems())
def test_init(self):
"""Trie init should create an empty trie."""
t = Compressed_Trie()
self.assertEqual(t.root.labels, [])
self.assertEqual(t.root.children, {})
self.assertEqual(t.root.key, "")
def test_non_zero(self):
"""__non_zero__ should cehck for any data in the trie."""
t = Compressed_Trie()
self.assertEqual(t.__nonzero__(), False)
self.assertEqual(self.trie.__nonzero__(), True)
def test_len(self):
"""__len__ should return the number of seqs in the trie."""
self.assertEqual(len(self.trie), 9)
def test_size(self):
"""size should return the number of nodes in the trie."""
self.assertEqual(self.trie.size(), 10)
def test_to_string(self):
"""_to_string should create a string representation."""
string_rep = """
key
{
\tkey a['5']
\t{
\t\tkey b['0']
\t\t{
\t\t\tkey ab['2']
\t\t\t{
\t\t\t\tkey a
\t\t\t\t{
\t\t\t\t\tkey a['4']
\t\t\t\t}
\t\t\t\t{
\t\t\t\t\tkey ba['1', '6']
\t\t\t\t}
\t\t\t}
\t\t}
\t}
}
{
\tkey bab['7']
\t{
\t\tkey a['3']
\t}
\t{
\t\tkey ba['8']
\t}
}
"""
self.assertEqual(str(self.trie), string_rep)
def test_insert_find(self):
"""An added key should be found by find."""
data = self.data
t = Compressed_Trie()
for (label, seq) in data.iteritems():
t.insert(seq, label)
for (label, seq) in data.iteritems():
self.assertEqual(label in t.find(seq), True)
self.assertEqual(t.find("abababa"), ["1","6"])
self.assertEqual(t.find("cacgchagc"), [])
def test_prefixMap(self):
"""prefix_map (Compressed_Trie) should map prefix strings."""
self.assertEqual(self.trie.prefixMap(),
{'1': ['6', '2', '0', '5'],
'8': ['7'],
'3': [],
'4': []})
def test_build_trie(self):
"""Build_trie should build trie from seqs."""
t = build_trie(self.data.iteritems())
self.assertTrue(isinstance(t, Compressed_Trie))
for (label, seq) in self.data.iteritems():
self.assertContains(t.find(seq), label)
self.assertEqual(t.find(""), [])
self.assertEqual(t.find("ccc"), [])
if __name__ == "__main__":
main()
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