Source Code for Module Bio.GA.Crossover.General

 1  """General functionality for crossover that doesn't apply. 
 2   
 3  This collects Crossover stuff that doesn't deal with any specific 
 4  type of crossover. 
 5  """ 
 6  # standard library 
 7  import random 
 8   
 9  # local stuff 
10  from Bio.GA.Organism import Organism 
11   
12   
13 -class SafeFitnessCrossover(object): 
14      """Perform crossovers, but do not allow decreases in organism fitness. 
15   
16      This doesn't actually do any crossover work, but instead relies on 
17      another class to do the crossover and just checks that newly created 
18      organisms do not have less fitness. This is useful for cases where 
19      crossovers can 
20      """ 
21 -    def __init__(self, actual_crossover, accept_less = 0.0): 
22          """Initialize to do safe crossovers. 
23   
24          Arguments: 
25   
26          o actual_crossover - A Crossover class which actually implements 
27          crossover functionality. 
28   
29          o accept_less - A probability to accept crossovers which 
30          generate less fitness. This allows you to accept some 
31          crossovers which reduce fitness, but not all of them. 
32          """ 
33          self._crossover = actual_crossover 
34          self._accept_less_percent = accept_less 
35          self._accept_less_rand = random.Random() 
36   
37 -    def do_crossover(self, org_1, org_2): 
38          """Perform a safe crossover between the two organism. 
39          """ 
40          new_org_1, new_org_2 = self._crossover.do_crossover(org_1, org_2) 
41   
42          return_orgs = [] 
43   
44          for start_org, new_org in ((org_1, new_org_1), 
45                                     (org_2, new_org_2)): 
46              new_org.recalculate_fitness() 
47   
48              # if the starting organism has a better fitness, 
49              # keep it, minding the acceptance of less favorable change policy 
50              if start_org.fitness > new_org.fitness: 
51                  accept_change = self._accept_less_rand.random() 
52                  if accept_change <= self._accept_less_percent: 
53                      return_orgs.append(new_org) 
54                  else: 
55                      return_orgs.append(start_org) 
56              else: 
57                  return_orgs.append(new_org) 
58   
59          assert len(return_orgs) == 2, "Should have two organisms to return." 
60   
61          return return_orgs 
62