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"""
This module provides code for various distance measures.
Functions:
euclidean Euclidean distance between two points
euclidean_py Pure Python implementation of euclidean.
"""
# XXX cosine distance
import math
try:
from Numeric import *
except ImportError, x:
raise ImportError, "This module requires NumPy"
from Bio import listfns
def euclidean(x, y):
"""euclidean(x, y) -> euclidean distance between x and y"""
if len(x) != len(y):
raise ValueError, "vectors must be same length"
#return sqrt(sum((x-y)**2))
# Optimization by John Corradi (JCorradi@msn.com)
d = x-y
return sqrt(dot(d, d))
def euclidean_py(x, y):
"""euclidean_py(x, y) -> euclidean distance between x and y"""
# lightly modified from implementation by Thomas Sicheritz-Ponten.
# This works faster than the Numeric implementation on shorter
# vectors.
if len(x) != len(y):
raise ValueError, "vectors must be same length"
sum = 0
for i in range(len(x)):
sum += (x[i]-y[i])**2
return math.sqrt(sum)
# Try and load C implementations of functions. If I can't,
# then just ignore and use the pure python implementations.
try:
from cdistance import *
except ImportError:
pass
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