def test_init_from_iterable(self):
b = Bitstring("0001")
b2 = Bitstring([1, 0, 0, 0])
b3 = Bitstring((True, False, False, False))
b4 = Bitstring("1")
self.assertEqual(b, b2)
self.assertEqual(b, b3)
self.assertNotEqual(b, b4)
def test_selected_loci_as_int(self):
b = Bitstring('110110')
pos_0 = b.selected_loci_as_int([0])
self.assertEqual(0, pos_0)
pos_123 = b.selected_loci_as_int([1, 2, 3])
self.assertEqual(3, pos_123)
pos_1 = b.selected_loci_as_int([1])
self.assertEqual(1, pos_1)
def test_selected_loci_as_int(self):
b = Bitstring('110110')
pos_0 = b.selected_loci_as_int([0])
self.assertEqual(0, pos_0)
pos_123 = b.selected_loci_as_int([1, 2, 3])
self.assertEqual(3, pos_123)
pos_1 = b.selected_loci_as_int([1])
self.assertEqual(1, pos_1)
def test_int(self):
b = Bitstring('110110')
c = Bitstring('0000')
d = Bitstring('')
e = Bitstring('10')
self.assertEqual(int(b), 54)
self.assertEqual(int(c), 0)
self.assertEqual(int(d), 0)
self.assertEqual(int(e), 2)
def test_eq(self):
b = Bitstring("10")
b2 = Bitstring("10")
b3 = Bitstring("100")
b4 = Bitstring("11")
self.assertTrue(b == b2)
self.assertTrue(b != b3)
self.assertTrue(b != b4)
s = "10"
self.assertFalse(b == s)
def test_iter(self):
b = Bitstring("01")
for pos, expected in zip(b, [True, False]):
self.assertEqual(pos, expected)
def test_hash(self):
b = Bitstring("000")
b_ = Bitstring("101")
self.assertSetEqual({b, b_}, {Bitstring("000"), Bitstring("101")})
def __init__(self, *args, **kwargs):
super(Organism, self).__init__(*args, **kwargs)
if (isinstance(self, Organism)
and not isinstance(self.value, Bitstring)):
raise ValueError("Bitstring Organisms must hold Bitstrings")
def _mutated_value(self):
"""
the mutate method of an organism calls the module
mutate and returns a new organism with the mutation
note: original organism is unchanged
"""
return self.value.single_step_mutant()
def _evaluate_fitness(self):
"""
fitness of this organism is the hamming distance of
its bitstring from a bitstring composed of all False's
"""
return 1 + sum(self.value)
default_organism = Organism(Bitstring(False for _ in range(10)))
def random_organism(length):
bits = [True, False]
sequence = [random.choice(bits) for _ in range(length)]
bs = Bitstring(sequence)
return Organism(bs)
def test_copy(self):
b = Bitstring("10101")
b_copy = copy.copy(b)
self.assertEqual(b, b_copy)
def random_organism(length):
bits = [True, False]
sequence = [random.choice(bits) for _ in range(length)]
bs = Bitstring(sequence)
return Organism(bs)
def test_hamming_distance(self):
b = Bitstring("10101")
b2 = Bitstring("10101")
b3 = Bitstring("01010")
self.assertEqual(b.hamming_distance(b2), 0)
self.assertEqual(b.hamming_distance(b3), 5)
def test_repr(self):
b = Bitstring("10")
b_as_str = repr(b)
b2 = eval(b_as_str)
self.assertEqual(b, b2)
def test_shift_by_bit(self):
for _ in range(10):
b = Bitstring("1010101")
mutant = mutate.shift_by_bit(b)
self.assertEqual(b.hamming_distance(mutant), 1)
def test_single_step_mutant(self):
bs = Bitstring("00")
mutant = bs.single_step_mutant()
self.assertNotEqual(bs, mutant)
def test_init(self):
b = Bitstring("01")
self.assertEqual(True, b[0])
self.assertEqual(False, b[1])
self.assertEqual(2, len(b))
def test_single_step_mutant(self):
bs = Bitstring("00")
mutant = bs.single_step_mutant()
self.assertNotEqual(bs, mutant)
def test_hamming_distance(self):
b = Bitstring("10101")
b2 = Bitstring("10101")
b3 = Bitstring("01010")
self.assertEqual(b.hamming_distance(b2), 0)
self.assertEqual(b.hamming_distance(b3), 5)
def test_flip_position(self):
b = Bitstring("00000")
b_mutated = bitstring.flip_position(b, 0)
self.assertEqual(b_mutated, Bitstring("00001"))
def setUp(self):
self.value_0 = Bitstring("000")
self.value_1 = Bitstring("001")
self.value_2 = Bitstring("111")
