def setUp(self):
unittest.TestCase.setUp(self)
#Creates a very basic branch-tree
self.s1 = Segment("A")
self.s2 = Segment("A")
self.s3 = Segment()
self.s4 = Segment("T")
self.s1.createBranch(self.s2)
self.s1.createBranch(self.s3)
self.s3.createBranch(self.s4)
def testLowerBoundSubstitutionCost(self):
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 1)
self.assertEqual(self.s2.lowerBoundSubstitutionCost(), 0)
self.assertEqual(self.s3.lowerBoundSubstitutionCost(), 0)
self.assertEqual(self.s4.lowerBoundSubstitutionCost(), 0)
s6 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 1)
s7 = Segment("G", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 2)
def testUpperBoundSubstitutionCost(self):
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 2)
self.assertEqual(self.s2.upperBoundSubstitutionCost(), 0)
self.assertEqual(self.s3.upperBoundSubstitutionCost(), 0)
self.assertEqual(self.s4.upperBoundSubstitutionCost(), 0)
s6 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 3)
s7 = Segment("G", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 4)
def testRearrangementAmbiguity(self):
self.assertEqual(self.s1.rearrangementAmbiguity(), 1)
self.assertEqual(self.s2.rearrangementAmbiguity(), 0)
self.assertEqual(self.s3.rearrangementAmbiguity(), 0)
self.s3.createBond(Segment().left)
self.assertEqual(self.s3.rearrangementAmbiguity(), 1)
self.assertEqual(self.s4.rearrangementAmbiguity(), 0)
def testSubstitutionAmbiguity(self):
self.assertEqual(self.s1.substitutionAmbiguity(), 0)
self.assertEqual(self.s2.substitutionAmbiguity(), 0)
self.assertEqual(self.s3.substitutionAmbiguity(), 0)
self.assertEqual(self.s4.substitutionAmbiguity(), 0)
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.substitutionAmbiguity(), 1)
def setUp(self):
unittest.TestCase.setUp(self)
#Creates a very basic branch-tree
self.s1 = Segment("A")
self.s2 = Segment("A")
self.s3 = Segment()
self.s4 = Segment("T")
self.s1.createBranch(self.s2)
self.s1.createBranch(self.s3)
self.s3.createBranch(self.s4)
def testAncestor(self):
self.assertEqual(self.s1.ancestor(), self.s1)
self.assertEqual(self.s2.ancestor(), self.s1)
self.assertEqual(self.s3.ancestor(), self.s1)
self.assertEqual(self.s4.ancestor(), self.s1)
self.assertEqual(self.s5.ancestor(), self.s1)
self.s3.createBond(Segment().left)
self.assertEqual(self.s4.ancestor(), self.s3)
self.assertEqual(self.s5.ancestor(), self.s3)
class SegmentTest(unittest.TestCase):
"""Tests the segment and associated label classes, including testing label functionality, but ignoring sides, which are
tested in sideTest.py"""
def setUp(self):
unittest.TestCase.setUp(self)
#Creates a very basic branch-tree
self.s1 = Segment("A")
self.s2 = Segment("A")
self.s3 = Segment()
self.s4 = Segment("T")
self.s1.createBranch(self.s2)
self.s1.createBranch(self.s3)
self.s3.createBranch(self.s4)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testChildren(self):
self.assertEqual(self.s1.children, set([ self.s2, self.s3 ]))
self.assertEqual(self.s2.children, set())
self.assertEqual(self.s3.children, set([ self.s4 ]))
self.assertEqual(self.s4.children, set())
def testParent(self):
self.assertEqual(self.s1.parent, None)
self.assertEqual(self.s2.parent, self.s1)
self.assertEqual(self.s3.parent, self.s1)
self.assertEqual(self.s4.parent, self.s3)
def testDeleteBranch(self):
self.s1.deleteBranch(self.s2)
self.assertEqual(self.s2.parent, None)
self.assertEqual(self.s1.children, set([ self.s3 ]))
self.s1.deleteBranch(self.s3)
self.assertEqual(self.s3.parent, None)
self.assertEqual(self.s1.children, set())
def testDisconnect(self):
self.s3.disconnect()
self.assertEqual(self.s3.parent, None)
self.assertEqual(self.s2.parent, self.s1)
self.assertEqual(self.s4.parent, self.s1)
self.assertEqual(self.s1.children, set([ self.s2, self.s4 ]))
self.assertEqual(self.s3.children, set())
def testStr(self):
self.assertEqual(str(self.s1), "A")
self.assertEqual(str(self.s2), "A")
self.assertEqual(str(self.s3), str(None))
self.assertEqual(str(self.s4), "T")
def testLabel(self):
self.assertEqual(self.s1.label, Label("A"))
self.assertEqual(self.s2.label, Label("A"))
self.assertEqual(self.s3.label, None)
self.assertEqual(self.s4.label, Label("T"))
def testDeleteLabel(self):
self.s1.deleteLabel()
self.assertEqual(self.s1.label, None)
def testAncestor(self):
self.assertEqual(self.s1.ancestor(), self.s1)
self.assertEqual(self.s2.ancestor(), self.s1)
self.assertEqual(self.s3.ancestor(), self.s1)
self.assertEqual(self.s4.ancestor(), self.s1)
self.s3.label = Label("A")
self.assertEqual(self.s4.ancestor(), self.s3)
def testLiftedLabels(self):
"""The lifted label function returns the segments that contain the lifting labels
"""
self.assertEqual(self.s1.liftedLabels(), set([ self.s2, self.s4 ]))
self.assertEqual(self.s2.liftedLabels(), set())
self.assertEqual(self.s3.liftedLabels(), set([ self.s4 ]))
self.assertEqual(self.s4.liftedLabels(), set())
def testNonTrivialLiftedLabels(self):
self.assertEqual(self.s1.nonTrivialLiftedLabels(), set([ self.s4 ]))
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.nonTrivialLiftedLabels(), set([ self.s4, s5 ]))
def testSubstitutionAmbiguity(self):
self.assertEqual(self.s1.substitutionAmbiguity(), 0)
self.assertEqual(self.s2.substitutionAmbiguity(), 0)
self.assertEqual(self.s3.substitutionAmbiguity(), 0)
self.assertEqual(self.s4.substitutionAmbiguity(), 0)
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.substitutionAmbiguity(), 1)
def testLowerBoundSubstitutionCost(self):
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 1)
self.assertEqual(self.s2.lowerBoundSubstitutionCost(), 0)
self.assertEqual(self.s3.lowerBoundSubstitutionCost(), 0)
self.assertEqual(self.s4.lowerBoundSubstitutionCost(), 0)
s6 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 1)
s7 = Segment("G", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 2)
def testUpperBoundSubstitutionCost(self):
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 2)
self.assertEqual(self.s2.upperBoundSubstitutionCost(), 0)
self.assertEqual(self.s3.upperBoundSubstitutionCost(), 0)
self.assertEqual(self.s4.upperBoundSubstitutionCost(), 0)
s6 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 3)
s7 = Segment("G", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 4)
def setUp(self):
unittest.TestCase.setUp(self)
#Creates a very basic branch-tree
self.s1 = Segment().left
self.s2 = Segment().left
self.s3 = Segment().left
self.s4 = Segment().left
self.s5 = Segment().left
self.s1.segment.createBranch(self.s2.segment)
self.s1.segment.createBranch(self.s3.segment)
self.s3.segment.createBranch(self.s4.segment)
self.s3.segment.createBranch(self.s5.segment)
self.s1B = Segment().left
self.s2B = Segment().left
self.s3B = Segment().left
self.s4B = Segment().left
self.s5B = Segment().left
self.s1B.segment.createBranch(self.s2B.segment)
self.s1B.segment.createBranch(self.s3B.segment)
self.s3B.segment.createBranch(self.s4B.segment)
self.s5B.segment.createBranch(self.s5B.segment)
self.s1.createBond(self.s1B)
self.s2.createBond(self.s2B)
self.s4.createBond(self.s4B)
self.s5.createBond(self.s5B.opposite)
class SideTest(unittest.TestCase):
"""Tests the segment and associated label classes, including testing label functionality, but ignoring sides, which are
tested in sideTest.py"""
def setUp(self):
unittest.TestCase.setUp(self)
#Creates a very basic branch-tree
self.s1 = Segment().left
self.s2 = Segment().left
self.s3 = Segment().left
self.s4 = Segment().left
self.s5 = Segment().left
self.s1.segment.createBranch(self.s2.segment)
self.s1.segment.createBranch(self.s3.segment)
self.s3.segment.createBranch(self.s4.segment)
self.s3.segment.createBranch(self.s5.segment)
self.s1B = Segment().left
self.s2B = Segment().left
self.s3B = Segment().left
self.s4B = Segment().left
self.s5B = Segment().left
self.s1B.segment.createBranch(self.s2B.segment)
self.s1B.segment.createBranch(self.s3B.segment)
self.s3B.segment.createBranch(self.s4B.segment)
self.s5B.segment.createBranch(self.s5B.segment)
self.s1.createBond(self.s1B)
self.s2.createBond(self.s2B)
self.s4.createBond(self.s4B)
self.s5.createBond(self.s5B.opposite)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testOpposite(self):
self.assertEquals(self.s1.opposite, self.s1.segment.right)
self.assertEquals(self.s2.opposite, self.s2.segment.right)
def testChildren(self):
self.assertEqual(set(self.s1.children()), set([ self.s2, self.s3 ]))
self.assertEqual(set(self.s2.children()), set())
self.assertEqual(set(self.s3.children()), set([ self.s4, self.s5 ]))
self.assertEqual(set(self.s4.children()), set())
def testParent(self):
self.assertEqual(self.s1.parent(), None)
self.assertEqual(self.s2.parent(), self.s1)
self.assertEqual(self.s3.parent(), self.s1)
self.assertEqual(self.s4.parent(), self.s3)
def testCreateAndDeleteBond(self):
self.assertEqual(self.s1.bond, self.s1B)
self.assertEqual(self.s1B.bond, self.s1)
self.s1.deleteBond()
self.assertEqual(self.s1.bond, None)
self.assertEqual(self.s1B.bond, None)
def testAncestor(self):
self.assertEqual(self.s1.ancestor(), self.s1)
self.assertEqual(self.s2.ancestor(), self.s1)
self.assertEqual(self.s3.ancestor(), self.s1)
self.assertEqual(self.s4.ancestor(), self.s1)
self.assertEqual(self.s5.ancestor(), self.s1)
self.s3.createBond(Segment().left)
self.assertEqual(self.s4.ancestor(), self.s3)
self.assertEqual(self.s5.ancestor(), self.s3)
def testIsJunction(self):
self.assertTrue(self.s1.isJunction())
self.assertTrue(not self.s2.isJunction())
self.assertTrue(self.s3.isJunction())
self.assertTrue(not self.s4.isJunction())
self.assertTrue(not self.s5.isJunction())
def testLiftedBonds(self):
"""The lifted bond function returns the segments that contain the lifting Bonds
"""
self.assertEqual(self.s1.liftedBonds(), set([ self.s2, self.s4, self.s5 ]))
self.assertEqual(self.s2.liftedBonds(), set())
self.assertEqual(self.s3.liftedBonds(), set([ self.s4, self.s5 ]))
self.assertEqual(self.s4.liftedBonds(), set())
self.assertEqual(self.s5.liftedBonds(), set())
def testNonTrivialLiftedBonds(self):
self.assertEqual(self.s1.nonTrivialLiftedBonds(), set([ self.s4, self.s5 ]))
self.assertEqual(self.s3.nonTrivialLiftedBonds(), set([ self.s4, self.s5 ]))
self.assertEqual(self.s4.nonTrivialLiftedBonds(), set())
def testRearrangementAmbiguity(self):
self.assertEqual(self.s1.rearrangementAmbiguity(), 1)
self.assertEqual(self.s2.rearrangementAmbiguity(), 0)
self.assertEqual(self.s3.rearrangementAmbiguity(), 0)
self.s3.createBond(Segment().left)
self.assertEqual(self.s3.rearrangementAmbiguity(), 1)
self.assertEqual(self.s4.rearrangementAmbiguity(), 0)
def testNonTrivialLiftedLabels(self):
self.assertEqual(self.s1.nonTrivialLiftedLabels(), set([self.s4]))
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.nonTrivialLiftedLabels(), set([self.s4, s5]))
class SegmentTest(unittest.TestCase):
"""Tests the segment and associated label classes, including testing label functionality, but ignoring sides, which are
tested in sideTest.py"""
def setUp(self):
unittest.TestCase.setUp(self)
#Creates a very basic branch-tree
self.s1 = Segment("A")
self.s2 = Segment("A")
self.s3 = Segment()
self.s4 = Segment("T")
self.s1.createBranch(self.s2)
self.s1.createBranch(self.s3)
self.s3.createBranch(self.s4)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testChildren(self):
self.assertEqual(self.s1.children, set([self.s2, self.s3]))
self.assertEqual(self.s2.children, set())
self.assertEqual(self.s3.children, set([self.s4]))
self.assertEqual(self.s4.children, set())
def testParent(self):
self.assertEqual(self.s1.parent, None)
self.assertEqual(self.s2.parent, self.s1)
self.assertEqual(self.s3.parent, self.s1)
self.assertEqual(self.s4.parent, self.s3)
def testDeleteBranch(self):
self.s1.deleteBranch(self.s2)
self.assertEqual(self.s2.parent, None)
self.assertEqual(self.s1.children, set([self.s3]))
self.s1.deleteBranch(self.s3)
self.assertEqual(self.s3.parent, None)
self.assertEqual(self.s1.children, set())
def testDisconnect(self):
self.s3.disconnect()
self.assertEqual(self.s3.parent, None)
self.assertEqual(self.s2.parent, self.s1)
self.assertEqual(self.s4.parent, self.s1)
self.assertEqual(self.s1.children, set([self.s2, self.s4]))
self.assertEqual(self.s3.children, set())
def testStr(self):
self.assertEqual(str(self.s1), "A")
self.assertEqual(str(self.s2), "A")
self.assertEqual(str(self.s3), str(None))
self.assertEqual(str(self.s4), "T")
def testLabel(self):
self.assertEqual(self.s1.label, Label("A"))
self.assertEqual(self.s2.label, Label("A"))
self.assertEqual(self.s3.label, None)
self.assertEqual(self.s4.label, Label("T"))
def testDeleteLabel(self):
self.s1.deleteLabel()
self.assertEqual(self.s1.label, None)
def testAncestor(self):
self.assertEqual(self.s1.ancestor(), self.s1)
self.assertEqual(self.s2.ancestor(), self.s1)
self.assertEqual(self.s3.ancestor(), self.s1)
self.assertEqual(self.s4.ancestor(), self.s1)
self.s3.label = Label("A")
self.assertEqual(self.s4.ancestor(), self.s3)
def testLiftedLabels(self):
"""The lifted label function returns the segments that contain the lifting labels
"""
self.assertEqual(self.s1.liftedLabels(), set([self.s2, self.s4]))
self.assertEqual(self.s2.liftedLabels(), set())
self.assertEqual(self.s3.liftedLabels(), set([self.s4]))
self.assertEqual(self.s4.liftedLabels(), set())
def testNonTrivialLiftedLabels(self):
self.assertEqual(self.s1.nonTrivialLiftedLabels(), set([self.s4]))
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.nonTrivialLiftedLabels(), set([self.s4, s5]))
def testSubstitutionAmbiguity(self):
self.assertEqual(self.s1.substitutionAmbiguity(), 0)
self.assertEqual(self.s2.substitutionAmbiguity(), 0)
self.assertEqual(self.s3.substitutionAmbiguity(), 0)
self.assertEqual(self.s4.substitutionAmbiguity(), 0)
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.substitutionAmbiguity(), 1)
def testLowerBoundSubstitutionCost(self):
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 1)
self.assertEqual(self.s2.lowerBoundSubstitutionCost(), 0)
self.assertEqual(self.s3.lowerBoundSubstitutionCost(), 0)
self.assertEqual(self.s4.lowerBoundSubstitutionCost(), 0)
s6 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 1)
s7 = Segment("G", parent=self.s1)
self.assertEqual(self.s1.lowerBoundSubstitutionCost(), 2)
def testUpperBoundSubstitutionCost(self):
s5 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 2)
self.assertEqual(self.s2.upperBoundSubstitutionCost(), 0)
self.assertEqual(self.s3.upperBoundSubstitutionCost(), 0)
self.assertEqual(self.s4.upperBoundSubstitutionCost(), 0)
s6 = Segment("T", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 3)
s7 = Segment("G", parent=self.s1)
self.assertEqual(self.s1.upperBoundSubstitutionCost(), 4)