def test_intersect(self):
a = PacBioBam.PositionInterval(2, 4)
b = PacBioBam.PositionInterval(3, 5)
c = PacBioBam.PositionInterval(6, 8)
d = PacBioBam.PositionInterval(1, 7)
e = PacBioBam.PositionInterval(5, 8)
# 0123456789
# a --
# b --
# c --
# d ------
# e ---
# self-intersection
self.assertTrue(a.Intersects(a))
# intersection is commutative
self.assertTrue(a.Intersects(b))
self.assertTrue(b.Intersects(a))
# covered implies intersection
self.assertTrue(d.Covers(a))
self.assertTrue(a.Intersects(d))
self.assertTrue(d.Intersects(a))
# c.start > b.stop (obvious disjoint)
self.assertFalse(b.Intersects(c))
# b.stop == e.start (intervals are right-open, so disjoint)
self.assertFalse(b.Intersects(e))
def test_copy(self):
interval1 = PacBioBam.PositionInterval(5, 8)
interval2 = PacBioBam.PositionInterval(interval1)
interval3 = interval1
self.assertEqual(interval1, interval1)
self.assertEqual(interval1, interval2)
self.assertEqual(interval1, interval3)
def test_modifiers(self):
interval1 = PacBioBam.PositionInterval(5, 8)
interval2 = PacBioBam.PositionInterval(interval1)
interval2.Start(2)
interval2.Stop(10)
self.assertNotEqual(interval1, interval2)
self.assertEqual(2, interval2.Start())
self.assertEqual(10, interval2.Stop())
def test_ctors(self):
empty = PacBioBam.PositionInterval()
single = PacBioBam.PositionInterval(4)
normal = PacBioBam.PositionInterval(5, 8)
self.assertEqual(0, empty.Start())
self.assertEqual(0, empty.Stop())
self.assertEqual(4, single.Start())
self.assertEqual(5, single.Stop())
self.assertEqual(5, normal.Start())
self.assertEqual(8, normal.Stop())
def test_length(self):
a = PacBioBam.PositionInterval(2, 4)
b = PacBioBam.PositionInterval(3, 5)
c = PacBioBam.PositionInterval(6, 8)
d = PacBioBam.PositionInterval(1, 7)
e = PacBioBam.PositionInterval(5, 8)
self.assertEqual(2, a.Length())
self.assertEqual(2, b.Length())
self.assertEqual(2, c.Length())
self.assertEqual(6, d.Length())
self.assertEqual(3, e.Length())
def test_equality(self):
empty = PacBioBam.PositionInterval()
empty2 = PacBioBam.PositionInterval()
singleton = PacBioBam.PositionInterval(4)
sameAsSingleton = PacBioBam.PositionInterval(4, 5)
normal = PacBioBam.PositionInterval(5, 8)
sameAsNormal = PacBioBam.PositionInterval(5, 8)
different = PacBioBam.PositionInterval(20, 40)
# self-equality
self.assertEqual(empty, empty)
self.assertEqual(singleton, singleton)
self.assertEqual(normal, normal)
self.assertEqual(different, different)
# same values
self.assertEqual(empty, empty2)
self.assertEqual(singleton, sameAsSingleton)
self.assertEqual(normal, sameAsNormal)
# different values
self.assertNotEqual(empty, singleton)
self.assertNotEqual(empty, normal)
self.assertNotEqual(empty, different)
self.assertNotEqual(singleton, normal)
self.assertNotEqual(normal, different)
def test_cover(self):
a = PacBioBam.PositionInterval(2, 4)
b = PacBioBam.PositionInterval(3, 5)
c = PacBioBam.PositionInterval(6, 8)
d = PacBioBam.PositionInterval(1, 7)
e = PacBioBam.PositionInterval(5, 8)
# 0123456789
# a --
# b --
# c --
# d ------
# e ---
# self-cover
self.assertTrue(a.Covers(a))
self.assertTrue(a.CoveredBy(a))
# basic covers/covered
self.assertTrue(b.CoveredBy(d))
self.assertTrue(d.Covers(b))
self.assertNotEqual(b, d)
self.assertFalse(b.Covers(d))
# completely disjoint
self.assertFalse(b.Covers(c))
self.assertFalse(c.Covers(b))
self.assertFalse(b.CoveredBy(c))
self.assertFalse(c.CoveredBy(b))
# b.stop == e.start
self.assertFalse(b.Covers(e))
self.assertFalse(b.CoveredBy(e))
# shared endpoint, start contained
self.assertTrue(e.Covers(c))
self.assertTrue(c.CoveredBy(e))
def test_validity(self):
a = PacBioBam.PositionInterval() # default ctor
b = PacBioBam.PositionInterval(0, 0) # start == stop (zero)
c = PacBioBam.PositionInterval(4, 4) # start == stop (nonzero)
d = PacBioBam.PositionInterval(0, 1) # start < stop (start is zero)
e = PacBioBam.PositionInterval(4,
5) # start < stop (start is nonzero)
f = PacBioBam.PositionInterval(5, 4) # start > stop
self.assertFalse(a.IsValid())
self.assertFalse(b.IsValid())
self.assertFalse(c.IsValid())
self.assertTrue(d.IsValid())
self.assertTrue(e.IsValid())
self.assertFalse(f.IsValid())