def test_multiple_search(self):
""" SARRAY: Search for all instances of a substring """
sa = SuffixArray(string='z123ABC123CBA256123')
assert_equal(sa.search_all('ABC'), [4])
assert_equal(sa.search_all('123'), [16, 7, 1])
assert_equal(sa.search_all('z'), [0])
assert_equal(sa.search_all('x'), [])
def test_lcp_array(self):
""" SARRAY: Check validity of LCP array """
string = "banana"
lcp_array = [-1, 1, 3, 0, 0, 2]
sarray = SuffixArray(string=string)
assert_equal(lcp_array, sarray.get_lcp_array())
string = "abc12abc15"
lcp_array = [-1, 1, 0, 0, 0, 4, 0, 3, 0, 2]
sarray = SuffixArray(string=string)
assert_equal(lcp_array, sarray.get_lcp_array())
def test_init_unicode(self):
""" SARRAY: Test initialisation of the Suffix Array using unicode string """
test_str = unicode('abcdef') + unichr(200)
s = test_str.encode("utf8")
sarray = SuffixArray(string=test_str)
test_array = []
for i in range(len(s)):
test_array.append(s[i:])
print "one", test_array
print "two", sarray.get_suffix_array()
assert_equal(sarray.get_suffix_array(), sorted(test_array))
def setup_class(self):
""" SARRAY: Initial configuration of TestSuffixArray, runs only once """
self.test_str = ["zabcada trip123", "abcadab", "abc123abc12abca"]
self.sarray1 = SuffixArray(string=self.test_str[0])
self.sarray2 = SuffixArray(string=self.test_str[1])
self.sarray3 = SuffixArray(string=self.test_str[2])
self.sa_range = range(len(self.sarray1.suffix_array))
class TestSuffixArray:
""" Testsing module for the Suffix Array """
@classmethod
def setup_class(self):
""" SARRAY: Initial configuration of TestSuffixArray, runs only once """
self.test_str = ["zabcada trip123", "abcadab", "abc123abc12abca"]
self.sarray1 = SuffixArray(string=self.test_str[0])
self.sarray2 = SuffixArray(string=self.test_str[1])
self.sarray3 = SuffixArray(string=self.test_str[2])
self.sa_range = range(len(self.sarray1.suffix_array))
@classmethod
def teardown_class(self):
""" SARRAY: Finalise testing, runs only once at the end """
pass
def test_init(self):
""" SARRAY: Test initialisation of the Suffix Array """
assert_equal(self.sarray1.str, self.test_str[0])
# Check that suffix array has been built properly
test_array = []
for i in self.sa_range:
test_array.append(self.test_str[0][i:])
assert_equal(self.sarray1.get_suffix_array(), sorted(test_array))
def test_init_unicode(self):
""" SARRAY: Test initialisation of the Suffix Array using unicode string """
test_str = unicode('abcdef') + unichr(200)
s = test_str.encode("utf8")
sarray = SuffixArray(string=test_str)
test_array = []
for i in range(len(s)):
test_array.append(s[i:])
print "one", test_array
print "two", sarray.get_suffix_array()
assert_equal(sarray.get_suffix_array(), sorted(test_array))
def test_init_greek(self):
""" SARRAY: Test loading file with non standard ascii characters """
tmp_str = get_smp_file('Greek-Lipsum.txt')
sarray = SuffixArray(string=tmp_str)
def test_array_as_str(self):
""" SARRAY: Test returnining suffix array as a string """
tmp = ""
for i in self.sa_range:
tmp = tmp + "%s %s\n" % (i, self.sarray1.get_sarray_item(i))
assert_equal(self.sarray1.return_array_as_string(), tmp)
def test_return_original_string(self):
""" SARRAY: Test returning original string provided to constructor """
assert_equal(self.sarray1.return_original_str(), self.test_str[0])
def test_search(self):
""" SARRAY: Search for substings """
assert_equal(self.sarray1.search(' '), 7) # search for a char within string
assert_equal(self.sarray1.search('trip'), 8) # search for a word within string
assert_equal(self.sarray1.search('z'), 0) # Search for character in the beginning
assert_equal(self.sarray1.search('za'), 0) # Search for 2 characters in the beginning
assert_equal(self.sarray1.search('3'), 14) # Seach for character in the end
assert_equal(self.sarray1.search('123'), 12) # Search for many characters in the end
assert_equal(self.sarray1.search('y'), -1) # Search for non existant character
def test_multiple_search(self):
""" SARRAY: Search for all instances of a substring """
sa = SuffixArray(string='z123ABC123CBA256123')
assert_equal(sa.search_all('ABC'), [4])
assert_equal(sa.search_all('123'), [16, 7, 1])
assert_equal(sa.search_all('z'), [0])
assert_equal(sa.search_all('x'), [])
def test_suffix_array_item(self):
""" SARRAY: Get suffix array items """
str = "abcadab"
sa = SuffixArray(str)
expected_array = ['ab', 'abcadab', 'adab', 'b', 'bcadab', 'cadab', 'dab']
for i in range(len(array)):
assert_equal(expected_array[i], array[i])
def test_lcp_array(self):
""" SARRAY: Check validity of LCP array """
string = "banana"
lcp_array = [-1, 1, 3, 0, 0, 2]
sarray = SuffixArray(string=string)
assert_equal(lcp_array, sarray.get_lcp_array())
string = "abc12abc15"
lcp_array = [-1, 1, 0, 0, 0, 4, 0, 3, 0, 2]
sarray = SuffixArray(string=string)
assert_equal(lcp_array, sarray.get_lcp_array())