def testSetItem(self):
chain = Chain(self.a[:])
chain[2] = 't'
element_2 = chain.data[2]
self.assertEqual(chain[2], element_2)
chain = Chain(self.a[:])
chain[0] = Hetero('U')
element_0 = chain.data[0]
self.assertEqual(chain[0], element_0)
chain = Chain(self.b[:])
chain[-1] = Hetero('c')
last_element = chain.data[-1]
self.assertEqual(chain[-1], last_element)
chain = Chain(self.b[:])
chain[1] = 'a'
element_1 = chain.data[1]
self.assertEqual(chain[1], element_1)
chain = Chain(self.c[:])
chain[5] = 'ser'
element_5 = chain.data[5]
self.assertEqual(chain[5], element_5)
def testSetItem(self):
chain = Chain(self.a[:])
chain[2] = "t"
element_2 = chain.data[2]
self.assertEqual(chain[2], element_2)
chain = Chain(self.a[:])
chain[0] = Hetero("U")
element_0 = chain.data[0]
self.assertEqual(chain[0], element_0)
chain = Chain(self.b[:])
chain[-1] = Hetero("c")
last_element = chain.data[-1]
self.assertEqual(chain[-1], last_element)
chain = Chain(self.b[:])
chain[1] = "a"
element_1 = chain.data[1]
self.assertEqual(chain[1], element_1)
chain = Chain(self.c[:])
chain[5] = "ser"
element_5 = chain.data[5]
self.assertEqual(chain[5], element_5)
def testLen(self):
bru = Hetero('bru')
self.assertEqual(len(bru), 3)
_14w = Hetero('14w')
self.assertEqual(len(_14w), 3)
a = Hetero('a')
self.assertEqual(len(a), 1)
ga = Hetero('ga')
self.assertEqual(len(ga), 2)
def testLen(self):
bru = Hetero("bru")
self.assertEqual(len(bru), 3)
_14w = Hetero("14w")
self.assertEqual(len(_14w), 3)
a = Hetero("a")
self.assertEqual(len(a), 1)
ga = Hetero("ga")
self.assertEqual(len(ga), 2)
def testEquals(self):
u = Hetero('u')
u1 = Hetero('u')
self.assertEqual(u, u1)
self.assertEqual(u, Hetero('U'))
self.assertNotEqual(u, Hetero('u1'))
self.assertNotEqual(u, Hetero('x'))
gna = Hetero('gna')
self.assertEqual(gna, Hetero('gNA'))
self.assertEqual(gna, Hetero('GnA'))
self.assertNotEqual(gna, Hetero('gnb'))
self.assertNotEqual(gna, Hetero('na'))
def testIndex(self):
chain = Chain(self.a[:])
index_g = chain.data.index(Hetero('g'))
self.assertEqual(chain.index('g'), index_g)
chain = Chain(self.b[:])
index_c = chain.data.index(Hetero('c'))
self.assertEqual(chain.index('c'), index_c)
chain = Chain(self.c[:])
index_met = chain.data.index(Hetero('met'))
self.assertEqual(chain.index('met'), index_met)
def testEquals(self):
u = Hetero("u")
u1 = Hetero("u")
self.assertEqual(u, u1)
self.assertEqual(u, Hetero("U"))
self.assertNotEqual(u, Hetero("u1"))
self.assertNotEqual(u, Hetero("x"))
gna = Hetero("gna")
self.assertEqual(gna, Hetero("gNA"))
self.assertEqual(gna, Hetero("GnA"))
self.assertNotEqual(gna, Hetero("gnb"))
self.assertNotEqual(gna, Hetero("na"))
def testIndex(self):
chain = Chain(self.a[:])
index_g = chain.data.index(Hetero("g"))
self.assertEqual(chain.index("g"), index_g)
chain = Chain(self.b[:])
index_c = chain.data.index(Hetero("c"))
self.assertEqual(chain.index("c"), index_c)
chain = Chain(self.c[:])
index_met = chain.data.index(Hetero("met"))
self.assertEqual(chain.index("met"), index_met)
def testCount(self):
chain = Chain(self.a[:])
num_a = chain.data.count(Hetero('a'))
self.assertEqual(chain.count('a'), num_a)
chain = Chain(self.b[:])
num_a = chain.data.count(Hetero('t'))
self.assertEqual(chain.count('t'), num_a)
chain = Chain(self.c[:])
num_a = chain.data.count(Hetero('leu'))
self.assertEqual(chain.count('leu'), num_a)
chain = Chain(self.c[:])
num_a = chain.data.count(Hetero('cys'))
self.assertEqual(chain.count('cys'), num_a)
def testCount(self):
chain = Chain(self.a[:])
num_a = chain.data.count(Hetero("a"))
self.assertEqual(chain.count("a"), num_a)
chain = Chain(self.b[:])
num_a = chain.data.count(Hetero("t"))
self.assertEqual(chain.count("t"), num_a)
chain = Chain(self.c[:])
num_a = chain.data.count(Hetero("leu"))
self.assertEqual(chain.count("leu"), num_a)
chain = Chain(self.c[:])
num_a = chain.data.count(Hetero("cys"))
self.assertEqual(chain.count("cys"), num_a)
def testDelItem(self):
chain = Chain(self.a[:])
elements = self.a.strip().split()
num_elements = len(elements)
num_t = chain.data.count(Hetero('t'))
del chain[4]
num_t_remaining = chain.data.count(Hetero('t'))
self.assertEqual(num_t_remaining, num_t - 1)
self.assertEqual(len(chain), num_elements - 1)
chain = Chain(self.a[:])
elements = self.a.strip().split()
num_elements = len(elements)
num_u = chain.data.count(Hetero('u'))
del chain[12]
num_u_remaining = 0
self.assertEqual(num_u_remaining, num_u - 1)
self.assertEqual(len(chain), num_elements - 1)
chain = Chain(self.b[:])
elements = self.b.strip().split()
num_elements = len(elements)
num_c = chain.data.count(Hetero('c'))
del chain[0]
num_c_remaining = chain.data.count(Hetero('c'))
self.assertEqual(num_c_remaining, num_c - 1)
self.assertEqual(len(chain), num_elements - 1)
chain = Chain(self.b[:])
elements = self.b.strip().split()
num_elements = len(elements)
num_g = chain.data.count(Hetero('t'))
del chain[6]
num_g_remaining = chain.data.count(Hetero('t'))
self.assertEqual(num_g_remaining, num_g - 1)
self.assertEqual(len(chain), num_elements - 1)
chain = Chain(self.c[:])
elements = self.c.strip().split()
num_elements = len(elements)
num_thr = chain.data.count(Hetero('thr'))
del chain[0]
num_thr_remaining = chain.data.count(Hetero('thr'))
self.assertEqual(num_thr_remaining, num_thr - 1)
self.assertEqual(len(chain), num_elements - 1)
def testAppend(self):
chain = Chain(self.a[:])
chain.append('U')
elements = self.a.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual('u', last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.a[:])
chain.append(Hetero('A'))
elements = self.a.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual('a', last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.b[:])
chain.append('t')
elements = self.b.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual('t', last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.b[:])
chain.append(Hetero('C'))
elements = self.b.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual('c', last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.c[:])
chain.append('ser')
elements = self.c.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual('ser', last_element.data)
self.assertEqual(len(chain), num_elements + 1)
def testRemove(self):
chain = Chain(self.a[:])
elements = self.a.strip().split()
num_elements = len(elements)
num_a = chain.data.count(Hetero('a'))
chain.remove('a')
num_a_remaining = chain.data.count(Hetero('a'))
self.assertEqual(num_a_remaining, num_a - 1)
self.assertEqual(len(chain), num_elements - 1)
chain = Chain(self.b[:])
elements = self.b.strip().split()
num_elements = len(elements)
num_b = chain.data.count(Hetero('t'))
chain.remove('t')
num_b_remaining = chain.data.count(Hetero('t'))
self.assertEqual(num_b_remaining, num_b - 1)
self.assertEqual(len(chain), num_elements - 1)
chain = Chain(self.c[:])
elements = self.c.strip().split()
num_elements = len(elements)
num_leu = chain.data.count(Hetero('leu'))
chain.remove('leu')
num_leu_remaining = chain.data.count(Hetero('leu'))
self.assertEqual(num_leu_remaining, num_leu - 1)
self.assertEqual(len(chain), num_elements - 1)
def testAppend(self):
chain = Chain(self.a[:])
chain.append("U")
elements = self.a.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual("u", last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.a[:])
chain.append(Hetero("A"))
elements = self.a.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual("a", last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.b[:])
chain.append("t")
elements = self.b.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual("t", last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.b[:])
chain.append(Hetero("C"))
elements = self.b.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual("c", last_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.c[:])
chain.append("ser")
elements = self.c.strip().split()
num_elements = len(elements)
last_element = chain.data[-1]
self.assertEqual("ser", last_element.data)
self.assertEqual(len(chain), num_elements + 1)
def testInsert(self):
chain = Chain(self.a[:])
i = 4
chain.insert(i, 'g')
elements = self.a.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual('g', target_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.a[:])
i = 0
chain.insert(i, 't')
elements = self.a.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual('t', target_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.b[:])
i = 9
chain.insert(i, Hetero('a'))
elements = self.a.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual('a', target_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.c[:])
i = 5
chain.insert(i, 'gln')
elements = self.c.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual('gln', target_element.data)
self.assertEqual(len(chain), num_elements + 1)
def testInsert(self):
chain = Chain(self.a[:])
i = 4
chain.insert(i, "g")
elements = self.a.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual("g", target_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.a[:])
i = 0
chain.insert(i, "t")
elements = self.a.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual("t", target_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.b[:])
i = 9
chain.insert(i, Hetero("a"))
elements = self.a.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual("a", target_element.data)
self.assertEqual(len(chain), num_elements + 1)
chain = Chain(self.c[:])
i = 5
chain.insert(i, "gln")
elements = self.c.strip().split()
num_elements = len(elements)
target_element = chain.data[i]
self.assertEqual("gln", target_element.data)
self.assertEqual(len(chain), num_elements + 1)