def testNoCoverage(self):
"""
If a scanned read has no landmarks or trig points, its coveredIndices
method must return the empty set.
"""
read = ScannedRead(AARead('id', 'AAA'))
self.assertEqual(set(), read.coveredIndices())
def testCoverageOfOneLandmarkPoint(self):
"""
If a scanned read has one landmark, its coveredIndices method must
return the indices of that landmark.
"""
read = ScannedRead(AARead('id', 'AAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
self.assertEqual({0, 1}, read.coveredIndices())
def testCoverageOfOneTrigPoint(self):
"""
If a scanned read has one trig point, its coveredIndices method must
return the index of that trig point.
"""
read = ScannedRead(AARead('id', 'AAA'))
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual({0}, read.coveredIndices())
def testCoverageOfTwoIdenticalTrigPoints(self):
"""
If a scanned read has two trig points that occur at the same index, its
coveredIndices method must return the common index of the trig point.
"""
read = ScannedRead(AARead('id', 'AAA'))
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual({0}, read.coveredIndices())
def testCoverageOfTwoTrigPoints(self):
"""
If a scanned read has two trig points, its coveredIndices method must
return the indices of those trig points.
"""
read = ScannedRead(AARead('id', 'AAA'))
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
trigPoint = TrigPoint('name', 'symbol', 1)
read.trigPoints.append(trigPoint)
self.assertEqual({0, 1}, read.coveredIndices())
def testCoverageOfTwoDifferentOverlappingLandmarkPoints(self):
"""
If a scanned read has two landmarks, its coveredIndices method must
return the indices of those two landmarks.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol1', 0, 5)
read.landmarks.append(landmark)
landmark = Landmark('name', 'symbol2', 4, 2)
read.landmarks.append(landmark)
self.assertEqual({0, 1, 2, 3, 4, 5}, read.coveredIndices())
