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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""General functionality for mutations.
"""
# standard library
import random
# local stuff
from Bio.GA.Organism import Organism
class SafeFitnessMutation(object):
"""Perform mutations, but do not allow decreases in organism fitness.
This doesn't actually do any mutation work, but just checks that
newly create organisms do not have lower fitnesses.
"""
def __init__(self, actual_mutation, accept_less=0.0):
"""Initialize to do safe mutations
Arguments:
o actual_mutation - A Mutation class which actually implements
mutation. functionality.
o accept_less - A probability to accept mutations which
generate lower fitness. This allows you to accept some
crossovers which reduce fitness, but not all of them.
"""
self._mutation = actual_mutation
self._accept_less_percent = accept_less
self._accept_less_rand = random.Random()
def mutate(self, org):
"""Perform safe mutation of the specified organism.
"""
new_org = self._mutation.mutate(org)
new_org.recalculate_fitness()
if org.fitness > new_org.fitness:
accept_less_chance = self._accept_less_rand.random()
if accept_less_chance <= self._accept_less_percent:
return new_org
else:
return org
else:
return new_org
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