Created
February 17, 2012 16:48
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generate Hamming graph H(n, 2)
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#!/usr/bin/env python | |
""" | |
Generate a Hamming Graph | |
""" | |
import networkx | |
import itertools | |
import logging | |
def hamming_binary(chromosome_len): | |
"""Generate a binary Hamming Graph, where each genotype is composed by chromosome_len bases and each base can take only two values. H(chromosome_len, 2). | |
steps to generate an Hamming graph: | |
* create 2^chromosome_len nodes, each for a different binary string | |
* for each node, find the connected nodes by flipping one position at a time. | |
""" | |
space = networkx.Graph() | |
# create all nodes | |
l = ["01"] * chromosome_len | |
all_nodes = itertools.product(*l) | |
all_nodes = [''.join(x) for x in all_nodes] | |
logging.debug(all_nodes) | |
space.add_nodes_from(all_nodes) | |
# for each node, find neighbors | |
for node in space.nodes(): | |
[space.add_edge(node, mutate_node(node, base)) for base in range(chromosome_len)] | |
return space | |
def mutate_node(node, n): | |
# wonder if there is some binary utils package for python | |
if node[n] == '0': | |
newbase = '1' | |
else: | |
newbase = '0' | |
new_node = node[0:n] + newbase + node[n+1:] | |
return new_node | |
if __name__ == '__main__': | |
logging.basicConfig(level=logging.DEBUG) | |
space = hamming_binary(5) |
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note the forked version by Brandon Invergo, which uses binary operators
https://gist.github.com/1854574