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Sourcecode: python-biopython version File versions

distance.py

00001 """
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

00018 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))

00027 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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