class DNAHistoryGraphTest(unittest.TestCase):
"""Tests the DNA history graph functions, particularly the acyclicity functions
"""
def setUp(self):
unittest.TestCase.setUp(self)
self.g = DNAHistoryGraph()
self.s1 = self.g.newSegment("A")
self.s2 = self.g.newSegment("T")
self.s3 = self.g.newSegment("T")
self.s4 = self.g.newSegment("A")
self.s5 = self.g.newSegment("A")
self.g.createBranch(self.s1, self.s2)
self.g.createBranch(self.s1, self.s3)
self.g.createBranch(self.s3, self.s4)
self.g.createBranch(self.s3, self.s5)
self.s1b = self.g.newSegment("A")
self.s2b = self.g.newSegment("A")
self.s3b = self.g.newSegment()
self.s4b = self.g.newSegment("T")
self.s5b = self.g.newSegment("T")
self.g.createBranch(self.s1b, self.s2b)
self.g.createBranch(self.s1b, self.s3b)
self.g.createBranch(self.s3b, self.s4b)
self.g.createBranch(self.s3b, self.s5b)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testInterpolateSegment(self):
#Test case where segment is root
self.assertEqual(self.s1.parent, None)
s6 = self.g.interpolateSegment(self.s1)
self.assertEqual(self.s1.parent, s6)
self.assertEqual(s6.children, set([ self.s1 ]))
#Test case where segment is not root
self.assertEqual(self.s2.parent, self.s1)
self.assertEqual(self.s1.children, set([ self.s2, self.s3 ]))
s6 = self.g.interpolateSegment(self.s2)
self.assertEqual(self.s2.parent, s6)
self.assertEqual(s6.children, set([ self.s2 ]))
self.assertEqual(self.s1.children, set([ s6, self.s3 ]))
def testPullDown(self):
s6 = self.g.pullDown(self.s1, [ self.s2, self.s3 ])
self.assertEqual(s6.parent, self.s1)
self.assertEqual(self.s1.children, set([ s6 ]))
self.assertEqual(s6.children, set([self.s2, self.s3 ]))
self.assertEqual(s6, self.s2.parent)
self.assertEqual(s6, self.s3.parent)
def testCreateBond(self):
self.g.createBond(self.s1.left, self.s1b.left)
self.assertEquals(self.s1.left.bond, self.s1b.left)
self.assertEquals(self.s1b.left.bond, self.s1.left)
self.g.createBond(self.s3.left, self.s4b.left)
self.assertEquals(self.s3.left.bond, self.s4b.left)
self.assertEquals(self.s4b.left.bond, self.s3.left)
try: #Try to make bond that violates acyclicity
self.g.createBond(self.s4.left, self.s3b.left)
self.assertTrue(False)
except RuntimeError:
pass
def testDeleteBond(self):
self.g.createBond(self.s1.left, self.s1b.left)
self.g.createBond(self.s2.left, self.s2b.left)
self.g.createBond(self.s3.left, self.s3b.left)
self.g.createBond(self.s4.left, self.s4b.left)
self.g.createBond(self.s5.left, self.s5b.left)
self.assertEquals(self.s3.left.bond, self.s3b.left)
self.assertEquals(self.s3b.left.bond, self.s3.left)
self.g.deleteBond(self.s3.left)
self.assertEquals(self.s3.left.bond, None)
self.assertEquals(self.s3b.left.bond, None)
self.g.deleteBond(self.s4.left)
self.g.deleteBond(self.s5.left)
self.g.createBond(self.s4.left, self.s3b.left)
self.assertEquals(self.s4.left.bond, self.s3b.left)
self.assertEquals(self.s3b.left.bond, self.s4.left)
self.g.deleteBond(self.s4.left)
self.g.createBond(self.s3.left, self.s4b.left)
self.assertEquals(self.s3.left.bond, self.s4b.left)
self.assertEquals(self.s4b.left.bond, self.s3.left)
def testAreSiblings(self):
pass
def testSubstitutionAmbiguity(self):
self.assertEquals(self.g.substitutionAmbiguity(), 3)
def testRearrangementAmbiguity(self):
pass
def testAmbiguity(self):
pass
def testLowerBoundSubstitutionCost(self):
self.assertEquals(self.g.lowerBoundSubstitutionCost(), 3)
def testUpperBoundSubstitutionCost(self):
self.assertEquals(self.g.upperBoundSubstitutionCost(), 6)
