def test_dcj_circular_excision(self):
a = Genome(Chromosome("ab"), Chromosome(".cd."))
b = Genome(Chromosome(".abcd."))
self.assertEquals(calculate_distance(a, b, method="dcj"), 1)
def test_dcj_default_example(self):
a = Genome(Chromosome("ab"), Chromosome(".cd."), Chromosome(".e."),
Chromosome("fg"))
b = Genome(Chromosome(".acD."), Chromosome("be"), Chromosome(".fg."))
self.assertEquals(calculate_distance(a, b, method="dcj"), 5)
def test_dcj_single_split(self):
a = Genome(Chromosome(".ab."))
b = Genome(Chromosome("ab"))
self.assertEquals(calculate_distance(a, b, method="dcj"), 1)
def test_dcj_backwards(self):
a = Genome(Chromosome("abc"))
b = Genome(Chromosome("cba"))
self.assertEquals(calculate_distance(a, b, method="dcj"), 2)
def test_dcj_intermediate_2_dcj(self):
a = Genome(Chromosome(".aBdCE."))
b = Genome(Chromosome(".abcde."))
self.assertEquals(calculate_distance(a, b, method="dcj"), 4)
def test_dcj_single_swap_dcj(self):
a = Genome(Chromosome(".acb."))
b = Genome(Chromosome(".abc."))
self.assertEquals(calculate_distance(a, b, method="dcj"), 2)
def test_dcj_single_a_indel(self):
a = Genome(Chromosome(".ac."))
b = Genome(Chromosome(".abc."))
self.assertEquals(calculate_distance(a, b, method="indel"), 1)