Source Code for Module Bio.GA.Mutation.General

 1  """General functionality for mutations. 
 2  """ 
 3  # standard library 
 4  import random 
 5   
 6  # local stuff 
 7  from Bio.GA.Organism import Organism 
 8   
 9   
10 -class SafeFitnessMutation(object): 
11      """Perform mutations, but do not allow decreases in organism fitness. 
12   
13      This doesn't actually do any mutation work, but just checks that 
14      newly create organisms do not have lower fitnesses. 
15      """ 
16 -    def __init__(self, actual_mutation, accept_less = 0.0): 
17          """Initialize to do safe mutations 
18   
19          Arguments: 
20   
21          o actual_mutation - A Mutation class which actually implements 
22          mutation. functionality. 
23   
24          o accept_less - A probability to accept mutations which 
25          generate lower fitness. This allows you to accept some 
26          crossovers which reduce fitness, but not all of them. 
27          """ 
28          self._mutation = actual_mutation 
29          self._accept_less_percent = accept_less 
30          self._accept_less_rand = random.Random() 
31   
32 -    def mutate(self, org): 
33          """Perform safe mutation of the specified organism. 
34          """ 
35          new_org = self._mutation.mutate(org) 
36          new_org.recalculate_fitness() 
37   
38          if org.fitness > new_org.fitness: 
39              accept_less_chance = self._accept_less_rand.random() 
40              if accept_less_chance <= self._accept_less_percent: 
41                  return new_org 
42              else: 
43                  return org 
44          else: 
45              return new_org 
46