def suffix_search_lcs(a, b):
# left and right bounds, max sizes
len_a, len_b = len(a) + 1, len(b) + 1
short = min(len(a), len(b))
tree = SuffixTree(False, [a])
# returns if there is a common substring of length m between a, b
def found_common(m):
return any(tree.findStringIdx(b[i-m:i]) for i in range(m, len_b))
# exponentially increase l and r
l, r = 0, 1
while r < len_a and found_common(r):
l, r = r + 1, r * 2
r = min(r, short)
# right-most binary search on if substring length is possible
while l <= r:
m = (l + r) // 2
if found_common(m):
l = m + 1
else:
r = m - 1
return r
def transform(self, s):
""" Burrows-Wheeler transform with SuffixTree """
assert self.EOS not in s, "Input string cannot contain null character ('%s')" % self.EOS
# add end of text marker
s += self.EOS
st = SuffixTree()
# construct a suffix tree O(n * log n)
# can also be done in O(n) time
st.add(s)
# walk inorder to find sorted suffixes
# only get the length of each suffix
lens = self._walk(st.root)
# as the last column letter will be left of the suffix
# this means it's len(suffix) + 1
# from the end of the input string s
r = [0] * len(lens)
for i in xrange(len(lens)):
l = lens[i]
if l == len(lens):
r[i] = self.EOS
else:
r[i] = s[-l - 1]
return ''.join(r)
def __init__(self, dna):
self.dna = dna
self.suffix_tree = SuffixTree(len(dna))
self.suffix_array = []
self.first_col = []
self.bwt = []
self.ltof = []
self.init_self()
def suffix_search_lcs(a, b):
# left and right bounds, max sizes
len_a, len_b = len(a) + 1, len(b) + 1
short = min(len(a), len(b))
tree = SuffixTree(True, [a])
print('Completed suffix tree')
# returns if there is a common substring of length m between a, b
def found_common(m):
return any(tree.findStringIdx(b[i - m:i]) for i in range(m, len_b))
# exponentially increase l and r
l, r = 0, 1
print(l, r)
while r < len_a and found_common(r):
l, r = r + 1, r * 2
print(l, r)
r = min(r, short)
print(l, r)
# right-most binary search on if substring length is possible
while l <= r:
m = (l + r) // 2
print(m)
if found_common(m):
l = m + 1
else:
r = m - 1
print('Longest Common Substrings:')
print('\n'.join(
set(b[i - r:i] for i in range(r, len_b)
if tree.findStringIdx(b[i - r:i]))))
return r
@dataclass
class Point:
lat: float
lon: float
def __hash__(self) -> int:
return hash((self.lat, self.lon))
def __eq__(self, o: object) -> bool:
return self.__hash__() == o.__hash__()
def __str__(self) -> str:
return f'{self.lat},{self.lon}'
s = SuffixTree()
s.generate(
(
Point(1,1),
Point(1,0),
Point(0,1),
Point(1,1),
Point(1,0),
Point(0,0),
)
)
# s.generate('MISSISSIPPI$')
# annotate graph for vizualization
for i in range(1, s.order()):
parent = s.parent_id(i)
'''
Created on Oct 23, 2018
@author: ckennington
'''
from stlm import STLM
from suffixtree import SuffixTree
from sequence import Sequence
trie = SuffixTree()
text = 'c a c a o'.split()
for w in text:
print('adding', w)
trie.add(w)
print('\n')
trie.print_tree()
print('\n')
trie.update_all_counts()
stlm = STLM(trie)
tests = [
'c a'.split(), 'c a o'.split(), 'a o'.split(), 'o'.split(), 'c'.split()
]
for test in tests:
seq = Sequence()
