def test_add_node_first(self):
"""add_node should correctly add first node and increase top index."""
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test._add_node(test_node)
self.assertEquals(len(test._path_stack), 1)
self.assertEquals(test._top_index, 0)
def test_findAllowedOption_currentAllowed(self):
"""Should return true when current option is allowed"""
#searchpath with no forbidden seqs, so anything should work
test = SearchPath(SearchPathHelper.alphabets)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
allowed_found = test.findAllowedOption()
self.assertEquals(allowed_found, True)
def test_get_nmer_len1(self):
"""get_nmer should return correct result for nmer 1 on full stack"""
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test_path._add_node(test_node)
correct_result = test_node.Value
real_result = test_path._get_nmer(1)
self.assertEquals(real_result, correct_result)
def test_get_top(self):
"""Should return a reference to top node on stack if there is one"""
test = SearchPath(SearchPathHelper.alphabets)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
topnode = SearchNode(SearchNodeHelper.alphabet)
test._add_node(topnode)
resultnode = test._get_top()
self.assertEquals(resultnode, topnode)
def test_get_nmer_tooLong(self):
"""get_nmer should return None for n > length of stack"""
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test_path._add_node(test_node)
#stack is 1 long. Ask for a 2 mer
real_result = test_path._get_nmer(2)
self.assertEquals(real_result, None)
def test_add_node_subsequent(self):
"""add_node should correctly add additional nodes and up top index."""
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test_node2 = SearchNode(SearchNodeHelper.alphabet)
test._add_node(test_node)
test._add_node(test_node2)
self.assertEquals(len(test._path_stack), 2)
self.assertEquals(test._top_index, 1)
def _fill_path(self, num_nodes, node_vals = []):
"""create a searchpath and add searchnodes; return path"""
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
for i in xrange(num_nodes):
curr_node = SearchNode(SearchNodeHelper.alphabet)
node_vals.append(curr_node.Value)
test._add_node(curr_node)
#next i
return test
def test_check_forbidden_seqs_none(self):
"""Should return False if path includes no forbidden seqs"""
#a seq that isn't in the standard fixed forbidden lib
allowed_seq = ["C", "U", "A", "T"]
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
#add more values, and cheat so as to make them something known
for known_val in allowed_seq:
curr_node = SearchNode(SearchNodeHelper.alphabet)
curr_node._options[0] = known_val #torque the node's innards
test._add_node(curr_node)
#next bad_val
real_result = test._check_forbidden_seqs()
self.assertEquals(real_result, False)
def test_check_forbidden_seqs_fixed(self):
"""Should return True if path includes a fixed forbidden seq"""
forbidden_seq = ["G", "U", "A"]
user_input = ["".join(forbidden_seq)]
user_input.extend(SearchPathHelper.standard_forbid_seq)
test = SearchPath(SearchPathHelper.alphabets, user_input)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
#add more values, and cheat so as to make them something forbidden
for bad_val in forbidden_seq:
curr_node = SearchNode(SearchNodeHelper.alphabet)
curr_node._options[0] = bad_val #torque the node's innards
test._add_node(curr_node)
#next bad_val
real_result = test._check_forbidden_seqs()
self.assertEquals(real_result, True)
def test_get_nmer(self):
"""get_nmer should return correct nmer for n <= length of stack"""
node_values = []
n = 4
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
for i in xrange(n+1):
curr_node = SearchNode(SearchNodeHelper.alphabet)
test_path._add_node(curr_node)
node_values.append(curr_node.Value)
#next
#get a nmer, and get the last n values that were put on stack;
#should be the same
real_result = test_path._get_nmer(n)
correct_result = "".join(node_values[-n:])
self.assertEquals(real_result, correct_result)
