Limnoria/src/utils/seq.py
2014-01-20 15:43:55 +01:00

96 lines
4.0 KiB
Python

###
# Copyright (c) 2002-2005, Jeremiah Fincher
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list of conditions, and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions, and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the author of this software nor the name of
# contributors to this software may be used to endorse or promote products
# derived from this software without specific prior written consent.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
###
def window(L, size):
"""list * size -> window iterable
Returns a sliding 'window' through the list L of size size."""
assert not isinstance(L, int), 'Argument order swapped: window(L, size)'
if size < 1:
raise ValueError('size <= 0 disallowed.')
for i in xrange(len(L) - (size-1)):
yield L[i:i+size]
def mapinto(f, L):
for (i, x) in enumerate(L):
L[i] = f(x)
def renumerate(L):
for i in xrange(len(L)-1, -1, -1):
yield (i, L[i])
def dameraulevenshtein(seq1, seq2):
"""Calculate the Damerau-Levenshtein distance between sequences.
This distance is the number of additions, deletions, substitutions,
and transpositions needed to transform the first sequence into the
second. Although generally used with strings, any sequences of
comparable objects will work.
Transpositions are exchanges of *consecutive* characters; all other
operations are self-explanatory.
This implementation is O(N*M) time and O(M) space, for N and M the
lengths of the two sequences.
>>> dameraulevenshtein('ba', 'abc')
2
>>> dameraulevenshtein('fee', 'deed')
2
It works with arbitrary sequences too:
>>> dameraulevenshtein('abcd', ['b', 'a', 'c', 'd', 'e'])
2
"""
# codesnippet:D0DE4716-B6E6-4161-9219-2903BF8F547F
# Conceptually, this is based on a len(seq1) + 1 * len(seq2) + 1 matrix.
# However, only the current and two previous rows are needed at once,
# so we only store those.
# Sourced from http://mwh.geek.nz/2009/04/26/python-damerau-levenshtein-distance/
oneago = None
thisrow = range(1, len(seq2) + 1) + [0]
for x in xrange(len(seq1)):
# Python lists wrap around for negative indices, so put the
# leftmost column at the *end* of the list. This matches with
# the zero-indexed strings and saves extra calculation.
twoago, oneago, thisrow = oneago, thisrow, [0] * len(seq2) + [x + 1]
for y in xrange(len(seq2)):
delcost = oneago[y] + 1
addcost = thisrow[y - 1] + 1
subcost = oneago[y - 1] + (seq1[x] != seq2[y])
thisrow[y] = min(delcost, addcost, subcost)
# This block deals with transpositions
if (x > 0 and y > 0 and seq1[x] == seq2[y - 1]
and seq1[x-1] == seq2[y] and seq1[x] != seq2[y]):
thisrow[y] = min(thisrow[y], twoago[y - 2] + 1)
return thisrow[len(seq2) - 1]
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