Source Code for Module Bio.GA.Evolver

 1  """Evolution Strategies for a Population. 
 2   
 3  Evolver classes manage a population of individuals, and are responsible 
 4  for taking care of the transition from one generation to the next. 
 5  """ 
 6  # standard modules 
 7  import sys 
 8   
 9   
10 -class SteadyStateEvolver(object): 
11      """Evolve a population in place. 
12   
13      This implements a Steady State GA, where the population of individuals 
14      is evolved in place. 
15      """ 
16 -    def __init__(self): 
17          raise NotImplementedError("Need to code this.") 
18   
19   
20 -class GenerationEvolver(object): 
21      """Evolve a population from generation to generation. 
22   
23      This implements a Generational GA, in which the population moves from 
24      generation to generation. 
25      """ 
26 -    def __init__(self, starting_population, selector): 
27          """Initialize the evolver. 
28   
29          Arguments: 
30   
31          o starting_population -- An initial set of individuals to begin 
32          the evolution process from. This should be a list of Organism 
33          objects. 
34   
35          o selector -- A Selection object that implements selection, along 
36          with mutation and crossover to select a new population from a 
37          given population. 
38          """ 
39          self._population = starting_population 
40          self._selector = selector 
41   
42 -    def evolve(self, stopping_criteria): 
43          """Evolve the population through multiple generations. 
44   
45          Arguments: 
46   
47          o stoppping_criteria -- A function which, when passed the current 
48          individuals in the population, will determine when to stop 
49          the evolution process. 
50   
51          Returns: 
52   
53          o The final evolved population. 
54          """ 
55          while not(stopping_criteria(self._population)): 
56              try: 
57                  # perform selection, mutation, crossover on the population 
58                  self._population = self._selector.select(self._population) 
59   
60                  # update the fitness of the new popultation 
61                  for organism in self._population: 
62                      organism.recalculate_fitness() 
63   
64              # dump out all of the organisms for debugging if the 
65              # evolution process is broken with a Control-C 
66              except KeyboardInterrupt: 
67                  # sort the population so we can look at duplicates 
68                  self._population.sort() 
69                  for org in self._population: 
70                      print org 
71                  sys.exit() 
72   
73          return self._population 
74