def _set_up_genetic_algorithm(self):
"""Overrideable function to set up the genetic algorithm parameters.
This functions sole job is to set up the different genetic
algorithm functionality. Since this can be quite complicated, this
allows cusotmizablity of all of the parameters. If you want to
customize specially, you can inherit from this class and override
this function.
"""
self.motif_generator = RandomMotifGenerator(self.alphabet)
self.mutator = SinglePositionMutation(mutation_rate=0.1)
self.crossover = SinglePointCrossover(crossover_prob=0.25)
self.repair = AmbiguousRepair(Schema(self.alphabet.alphabet_matches),
4)
self.base_selector = TournamentSelection(self.mutator, self.crossover,
self.repair, 2)
self.selector = DiversitySelection(self.base_selector,
self.motif_generator.random_motif)
def setUp(self):
self.selector = DiversitySelection(NoSelection(), random_genome)
