def __init__(self, witnesses):
self.witnesses = witnesses
self.tokenindex = TokenIndex(witnesses)
self.tokenindex.prepare()
self.lcp_intervals = self.tokenindex.split_lcp_array_into_intervals()
global_maximum_score = calculate_maximum(self.lcp_intervals)
self.root = DecisionNode(global_maximum_score)
def test_witness_ranges_hermans_case(self):
collation = Collation()
collation.add_plain_witness("W1", "a b c d F g h i ! K ! q r s t")
collation.add_plain_witness("W2", "a b c d F g h i ! q r s t")
token_index = TokenIndex(collation.witnesses)
token_index.prepare()
self.assertEquals(RangeSet("0-14"),
token_index.get_range_for_witness("W1"))
self.assertEquals(RangeSet("16-28"),
token_index.get_range_for_witness("W2"))
def testTokenArrayMarkersWithThreeWitnesses(self):
collation = Collation()
collation.add_plain_witness("W1", "interesting nice huh")
collation.add_plain_witness("W2", "very nice right")
collation.add_plain_witness("W3", "especially interesting")
token_index = TokenIndex(collation.witnesses)
token_index.prepare()
self.assertTokenArray(
"interesting nice huh $0 very nice right $1 especially interesting",
token_index)
def test_token_array_hermans_case(self):
collation = Collation()
collation.add_plain_witness("W1", "a b c d F g h i ! K ! q r s t")
collation.add_plain_witness("W2", "a b c d F g h i ! q r s t")
token_index = TokenIndex(collation.witnesses)
token_index.prepare()
# $ is meant to separate witnesses here
self.assertTokenArray(
"a b c d F g h i ! K ! q r s t $0 a b c d F g h i ! q r s t",
token_index)
def test_lcp_intervals_number_of_witnesses_Hermans_case(self):
collation = Collation()
collation.add_plain_witness("W1", "a b c d F g h i ! K ! q r s t")
collation.add_plain_witness("W2", "a b c d F g h i ! q r s t")
collation.add_plain_witness("W3", "a b c d E g h i ! q r s t")
token_index = TokenIndex(collation.witnesses)
token_index.prepare()
intervals = token_index.split_lcp_array_into_intervals()
potential_block = intervals[1] # ! q r s t
self.assertEqual(3, potential_block.number_of_witnesses)
def testCaseDanielStoekl(self):
collation = Collation()
collation.add_plain_witness("W1", "a b c d e")
collation.add_plain_witness("W2", "a e c d")
collation.add_plain_witness("W3", "a d b")
token_index = TokenIndex(collation.witnesses)
token_index.prepare()
# Note: the suffix array can have multiple forms
# outcome of sorting is not guaranteed
# however the LCP array is fixed we can assert that
self.assertEquals(
array('i', [0, 0, 0, 1, 1, 0, 1, 0, 2, 0, 1, 1, 0, 1]),
token_index.get_lcp_array())
def test_filter_potential_blocks(self):
collation = Collation()
collation.add_plain_witness("W1", "a a")
collation.add_plain_witness("w2", "a")
token_index = TokenIndex(collation.witnesses)
token_index.prepare()
intervals = token_index.split_lcp_array_into_intervals()
# expectations
# There is one interval with length 1, number of occurrences 3, number of witnesses: 2
a_interval = intervals[0] # a
self.assertEqual(2, a_interval.number_of_witnesses)
self.assertEqual(1, a_interval.length)
self.assertEqual(3, a_interval.number_of_occurrences)
def setUp(self):
# we need to create witnesses
# 1: a, b, c, d, e
# 2: a, e, c, d
# 3: a, d, b
a = Witness({'id': 'A', 'content': "a b c d e"})
b = Witness({'id': 'B', 'content': "a e c d"})
c = Witness({'id': 'C', 'content': "a d b"})
self.witnesses = [a, b, c]
self.tokenindex = TokenIndex(self.witnesses)
self.tokenindex.prepare()
def testCaseDanielStoeklLCPIntervals(self):
collation = Collation()
collation.add_plain_witness("W1", "a b c d e")
collation.add_plain_witness("W2", "a e c d")
collation.add_plain_witness("W3", "a d b")
token_index = TokenIndex(collation.witnesses)
token_index.prepare()
blocks = token_index.split_lcp_array_into_intervals()
self.assertLCP_Interval(2, 1, 3, 3, blocks[0]) # a
self.assertLCP_Interval(5, 1, 2, 2, blocks[1]) # b
self.assertLCP_Interval(7, 2, 2, 2, blocks[2]) # c d
self.assertLCP_Interval(9, 1, 3, 3, blocks[3]) # d
self.assertLCP_Interval(12, 1, 2, 2, blocks[4]) # e
self.assertEquals(5, len(blocks))
def __init__(self,
collation,
near_match=False,
debug_scores=False,
detect_transpositions=False,
properties_filter=None):
self.collation = collation
self.debug_scores = debug_scores
self.detect_transpositions = detect_transpositions
self.token_index = TokenIndex(collation.witnesses)
self.scorer = Scorer(self.token_index,
near_match=near_match,
properties_filter=properties_filter)
self.align_function = self._align_table
def __init__(self,
collation,
near_match=False,
debug_scores=False,
detect_transpositions=False,
properties_filter=None):
self.scorer = Scorer()
self.collation = collation
self.debug_scores = debug_scores
self.detect_transpositions = detect_transpositions
self.properties_filter = properties_filter
self.token_index = TokenIndex(collation.witnesses)
self.token_position_to_vertex = {}
self.added_witness = []
self.omitted_base = []
self.vertex_array = []
self.cells = [[]]
