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tools_karkkainen_sanders.py
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tools_karkkainen_sanders.py
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#! /usr/bin/python
# -*- coding: utf-8 -*-
from array import array
def radixpass(a, b, r, n, k):
'''a : word to sort
b : sorted words
r : initial string
n : input size
k : alphabet size'''
c = array("i", [0] * (k + 1))
for i in xrange(n):
c[r[a[i]]] += 1
somme = 0
for i in xrange(k + 1):
freq, c[i] = c[i], somme
somme += freq
for i in xrange(n):
b[c[r[a[i]]]] = a[i]
c[r[a[i]]] += 1
def simple_kark_sort(s):
alphabet = [None] + sorted(set(s))
k = len(alphabet)
t = dict((c, i) for i, c in enumerate(alphabet))
n = len(s)
SA = array('i', [0] * (n + 3))
s = array('i', [t[c] for c in s] + [0] * 3)
kark_sort(s, SA, n, k)
return SA
def direct_kark_sort(s):
alphabet = [None] + sorted(set(s))
k = len(alphabet)
n = len(s)
t = dict((c, i) for i, c in enumerate(alphabet))
SA = array('i', [0] * (n + 3))
kark_sort(array('i', [t[c] for c in s] + [0] * 3), SA, n, k)
return SA[:n]
def kark_sort(s, SA, n, K):
'''s : word to sort
SA : result
n : len of s
K : alphabet size'''
n0 = (n + 2) / 3
n1 = (n + 1) / 3
n2 = n / 3
n02 = n0 + n2
SA12 = array('i', [0] * (n02 + 3))
SA0 = array('i', [0] * n0)
s12 = [i for i in xrange(n + (n0 - n1)) if i % 3]
s12.extend([0] * 3)
s12 = array('i', s12)
radixpass(s12, SA12, s[2:], n02, K)
radixpass(SA12, s12, s[1:], n02, K)
radixpass(s12, SA12, s, n02, K)
name = 0
c0, c1, c2 = -1, -1, -1
for i in xrange(n02):
if s[SA12[i]] != c0 or s[SA12[i] + 1] != c1 or s[SA12[i] + 2] != c2:
name += 1
c0 = s[SA12[i]]
c1 = s[SA12[i] + 1]
c2 = s[SA12[i] + 2]
if SA12[i] % 3 == 1:
s12[SA12[i] / 3] = name
else:
s12[SA12[i] / 3 + n0] = name
if name < n02:
kark_sort(s12, SA12, n02, name + 1)
for i in xrange(n02):
s12[SA12[i]] = i + 1
else:
for i in xrange(n02):
SA12[s12[i] - 1] = i
s0 = array('i', [SA12[i] * 3 for i in xrange(n02) if SA12[i] < n0])
radixpass(s0, SA0, s, n0, K)
p = j = k = 0
t = n0 - n1
while k < n:
i = SA12[t] * 3 + 1 if SA12[t] < n0 else (SA12[t] - n0) * 3 + 2
j = SA0[p] if p < n0 else 0
if SA12[t] < n0:
test = (s12[SA12[t] + n0] <= s12[j / 3]) if(
s[i] == s[j]) else (s[i] < s[j])
elif(s[i] == s[j]):
test = s12[SA12[t] - n0 + 1] <= s12[j / 3 + n0] if(
s[i + 1] == s[j + 1]) else s[i + 1] < s[j + 1]
else:
test = s[i] < s[j]
if(test):
SA[k] = i
t += 1
if t == n02:
k += 1
while p < n0:
SA[k] = SA0[p]
p += 1
k += 1
else:
SA[k] = j
p += 1
if p == n0:
k += 1
while t < n02:
SA[k] = (SA12[t] * 3) + 1 if SA12[
t] < n0 else ((SA12[t] - n0) * 3) + 2
t += 1
k += 1
k += 1
def LCP(s, suffix_array):
'''
return LCP array that LCP[i] is the longest common prefix
between s[SA[i]] and s[SA[i+1]]
'''
n = len(s)
rank = array('i', [0] * n)
LCP = array('i', [0] * n)
for i in xrange(n):
rank[suffix_array[i]] = i
l = 0
for j in xrange(n):
l = max(0, l - 1)
i = rank[j]
j2 = suffix_array[i - 1]
if i:
while l + j < n and l + j2 < n and s[j + l] == s[j2 + l]:
l += 1
LCP[i - 1] = l
else:
l = 0
return LCP