def testFindWithMarginZeroAndMarginPresentBothSides(self):
"""
A finder must find features when a zero margin is specified and there
is a margin on both sides.
"""
read = AARead('id', 'MFRRRFRRRFM')
landmark = AlphaHelix()
result = list(landmark.findWithMargin(read, 0))
self.assertEqual([Landmark('AlphaHelix', 'A', 1, 9, 2)], result)
def testFindWithMarginInsufficientMarginLeft(self):
"""
A finder must not return a feature that has insufficient margin
to the left.
"""
read = AARead('id', 'MMFRRRFRRRF')
landmark = AlphaHelix()
result = list(landmark.findWithMargin(read, 2))
self.assertEqual([], result)
def testFindWithMarginZeroAndNoMarginPresent(self):
"""
A finder must find features when a zero margin is specified and there
is no margin present.
"""
read = AARead('id', 'FRRRFRRRF')
landmark = AlphaHelix()
result = list(landmark.findWithMargin(read, 0))
self.assertEqual([Landmark('AlphaHelix', 'A', 0, 9, 2)], result)
def testFindWithMarginSufficientMargin(self):
"""
A finder must return a feature that has sufficient margin on both
sides.
"""
read = AARead('id', 'MMFRRRFRRRFMM')
landmark = AlphaHelix()
result = list(landmark.findWithMargin(read, 2))
self.assertEqual([Landmark('AlphaHelix', 'A', 2, 9, 2)], result)
def testNegativeMargin(self):
"""
If a negative margin is passed to findWithMargin, a ValueError must be
raised.
"""
read = AARead('id', 'FRRRFRRRF')
landmark = AlphaHelix()
error = '^Margin value \(-1\) is less than zero\.$'
six.assertRaisesRegex(self, ValueError, error, list,
landmark.findWithMargin(read, -1))
def testRestore(self):
"""
The restore method must produce the same parameter values that were
present in a DatabaseParameters instance when it is saved.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs],
distanceBase=3.0,
featureLengthBase=3.9,
limitPerLandmark=10,
maxDistance=77,
minDistance=66,
randomLandmarkDensity=0.1,
randomTrigPointDensity=0.9)
fp = StringIO()
dbParams.save(fp)
fp.seek(0)
result = DatabaseParameters.restore(fp)
self.assertEqual([AlphaHelix(), BetaStrand()], result.landmarkFinders)
self.assertEqual([Peaks(), Troughs()], result.trigPointFinders)
self.assertEqual(3.0, result.distanceBase)
self.assertEqual(3.9, result.featureLengthBase)
self.assertEqual(10, result.limitPerLandmark)
self.assertEqual(77, result.maxDistance)
self.assertEqual(66, result.minDistance)
self.assertEqual(0.1, result.randomLandmarkDensity)
self.assertEqual(0.9, result.randomTrigPointDensity)
def testNotEqual(self):
"""
Different finders must not compare equal.
"""
self.assertNotEqual(AlphaHelix(), BetaStrand())
def testEqual(self):
"""
Two identical finders must compare equal.
"""
self.assertEqual(AlphaHelix(), AlphaHelix())