class DNA_Test(unittest.TestCase):
nucleotides = Nucleotides(set(string.printable))
def test_dna_with_same_structure_are_equal(self):
dna1 = DNA("abcd")
dna2 = DNA("abcd")
self.assertEquals(dna1, dna2)
self.assertEquals(dna1.__hash__(), dna2.__hash__())
def test_dna_with_different_structure_are_not_equal(self):
dna2 = DNA("abcde")
self.assertNotEqual(DNA("abcd"), dna2)
self.assertNotEqual(DNA("abcd").__hash__(), dna2.__hash__())
def test_fitness_of_dna(self):
dna1 = DNA("abcd")
dna2 = DNA("abef")
self.assertEqual(dna1.measure_fitness(dna2), 2)
def test_dna_mutation(self):
dna = DNA("asdfghjkzxcvbnm")
mutated_dna = dna.mutate(20, self.nucleotides)
self.assertNotEqual(dna, mutated_dna)
self.assertEquals(len(dna.structure), len(mutated_dna.structure))
def test_dna_crossover(self):
dna1 = DNA("asdfghjkl")
dna2 = DNA("qwertyuio")
crossover_points = 2
child1 = dna1.crossover(dna2, crossover_points)
child2 = dna2.crossover(dna1, crossover_points)
self.assertNotEqual(child1, child2)
self.assertEqual(len(child1.structure), len(child2.structure))
class DNA(object):
nucleotides = Nucleotides(string.printable)
def __init__(self, structure):
self.structure = structure
def __eq__(self, other):
return self.structure == other.structure
def __hash__(self):
return self.structure.__hash__()
def measure_fitness(self, target):
fitness = 0
for this, other in zip(self.structure, target.structure):
if this == other:
fitness += 1
return fitness
def mutate(self, percentage=10, space_of_possibilities=nucleotides):
original_structure = list(self.structure)
mutate_indices = self.__generate_mutable_indices(percentage)
mutation_values = self.__generate_random_mutation(
space_of_possibilities, percentage)
mutated_structure = generate_mutated_structure(original_structure,
mutate_indices,
mutation_values)
return DNA(mutated_structure)
def crossover(self, other, crossover_points=2):
crossover_points = self.__generate_crossover_points(crossover_points)
child_structure = self.__generate_breed(crossover_points, other)
return DNA(child_structure)
def __generate_random_mutation(self, nucleotides, percentage):
mutate_count = self.__calculate_mutate_count(percentage)
nucleotides_values = nucleotides.create(mutate_count)
return nucleotides_values
def __generate_mutable_indices(self, percentage):
mutate_count = self.__calculate_mutate_count(percentage)
mutate_indices = random.sample(xrange(len(self.structure)),
mutate_count)
return mutate_indices
def __calculate_mutate_count(self, percentage):
mutate_count = len(self.structure) * percentage / 100
return mutate_count
def __generate_crossover_points(self, crossover_points):
crossover_indices = random.sample(xrange(len(self.structure)),
crossover_points)
crossover_indices.sort()
return crossover_indices
def __generate_breed(self, indices, other):
return self.structure[:indices[0]] + \
other.structure[indices[0]:indices[1]] + \
self.structure[indices[1]:]
def _initialise(self, target_string):
target_length = len(target_string)
nucleotides = Nucleotides(string.printable)
DNA.nucleotides = nucleotides
population_initialise = PopulationInitialise(nucleotides)
first_population = population_initialise.create(
population_size=self.population_size, structure_size=target_length)
first_generation = Generation(1, first_population)
return [first_generation]
def test_nucleotides_with_same_space_are_equal(self):
space1 = set("asdfghjk")
space2 = set("qwertyui")
nucleotides1 = Nucleotides(space1)
nucleotides2 = Nucleotides(space2)
self.assertNotEqual(nucleotides1, nucleotides2)
self.assertNotEqual(nucleotides1.__hash__(), nucleotides2.__hash__())
def test_initialise_population(self):
nucleotides = Nucleotides(set(string.printable))
population_initialise = PopulationInitialise(nucleotides)
population = population_initialise.create(population_size=10,
structure_size=500)
self.assertEquals(population.size, 10)
def test_nucleotides_with_same_space_are_equal(self):
space = set("asdfghjk")
nucleotides1 = Nucleotides(space)
nucleotides2 = Nucleotides(space)
self.assertEquals(nucleotides1, nucleotides2)
self.assertEquals(nucleotides1.__hash__(), nucleotides2.__hash__())
def test_nucleotides_generate_structure_greater_than_available_space(self):
space = set("asdfghj")
nucleotides = Nucleotides(space)
structure = nucleotides.create(size=10)
self.assertEquals(len(structure), 10)
def test_nucleotides_generate_structure(self):
space = set("asdfghjkiytfvygjmv")
nucleotides = Nucleotides(space)
structure = nucleotides.create(size=10)
self.assertEquals(len(structure), 10)