def testEmpty(self):
"""
If a combined feature list has no landmarks or trig points, its nearest
method should not generate any features.
"""
cfl = CombinedFeatureList([], [])
self.assertEqual([], list(cfl.nearest(0)))
def testFindOneMinDistance(self):
"""
If a combined feature list has one of two landmarks and trig points
inside the minDistance, find one.
"""
landmark = Landmark('name1', 'L', 0, 1)
trigPoint = TrigPoint('name2', 'T', 10)
cfl = CombinedFeatureList([landmark], [trigPoint])
result = list(cfl.nearest(8, minDistance=5))
self.assertEqual([landmark], result)
def testFindNoneMinDistance(self):
"""
If a combined feature list has no landmarks and trig points beyond the
minDistance, find none.
"""
landmark = Landmark('name1', 'L', 0, 1)
trigPoint = TrigPoint('name2', 'T', 10)
cfl = CombinedFeatureList([landmark], [trigPoint])
result = list(cfl.nearest(6, minDistance=10))
self.assertEqual([], result)
def testNothingInRange(self):
"""
If a combined feature list has no landmarks or trig points within range
of the offset passed to its nearest method, the method should not
generate any features.
"""
landmark1 = Landmark('name1', 'L1', 0, 1)
landmark2 = Landmark('name2', 'L2', 10, 1)
cfl = CombinedFeatureList([landmark1, landmark2], [])
self.assertEqual([], list(cfl.nearest(5, maxDistance=2)))
def testFindOneMinDistanceMaxDistance(self):
"""
If a combined feature list has three landmarks and trig points, one
outside the minDistance, one outside the maxDistance, find one.
"""
trigPoint1 = TrigPoint('name2', 'T', 0)
landmark = Landmark('name1', 'L', 5, 1)
trigPoint2 = TrigPoint('name3', 'T', 8)
cfl = CombinedFeatureList([landmark], [trigPoint1, trigPoint2])
result = list(cfl.nearest(5, maxDistance=4, minDistance=1))
self.assertEqual([trigPoint2], result)
def testFindAllMinDistance(self):
"""
If a combined feature list has all landmarks and trig points beyond the
minDistance, find all, with the landmarks first.
"""
landmark = Landmark('name1', 'L', 0, 1)
trigPoint1 = TrigPoint('name2', 'T', 10)
trigPoint2 = TrigPoint('name3', 'T', 11)
cfl = CombinedFeatureList([landmark], [trigPoint1, trigPoint2])
result = list(cfl.nearest(6, minDistance=1))
self.assertEqual([landmark, trigPoint1, trigPoint2], result)
def testFindTrigPointAndLandmarkMaxDistance(self):
"""
If a combined feature list has one landmark and one trig point
with only the trig point within the passed max distance, the nearest
method should yield just the trig point.
"""
landmark = Landmark('name1', 'L', 0, 1)
trigPoint = TrigPoint('name2', 'T', 10)
cfl = CombinedFeatureList([landmark], [trigPoint])
result = list(cfl.nearest(6, maxDistance=5))
self.assertEqual([trigPoint], result)
def testFindLandmarkAndTrigPoint(self):
"""
If a combined feature list has one landmark and one trig point within
range, with the landmark closest to the passed offset, the nearest
method should yield them both, with the landmark first.
"""
landmark = Landmark('name1', 'L', 0, 1)
trigPoint = TrigPoint('name2', 'T', 10)
cfl = CombinedFeatureList([landmark], [trigPoint])
result = list(cfl.nearest(4))
self.assertEqual([landmark, trigPoint], result)
def testNearestFindsZeroDistanceTrigPoint(self):
"""
If a combined feature list has one trig point and the offset of that
trig point is given to its nearest method, that trig point should be
generated.
"""
trigPoint = TrigPoint('name', 'T', 10)
cfl = CombinedFeatureList([], [trigPoint])
result = list(cfl.nearest(10, maxDistance=0))
self.assertEqual(1, len(result))
self.assertIs(trigPoint, result[0])
def testNearestFindsZeroDistanceLandmark(self):
"""
If a combined feature list has one landmark and the offset of that
landmark is given to its nearest method, that landmark should be
generated.
"""
landmark = Landmark('name', 'L', 10, 1)
cfl = CombinedFeatureList([landmark], [])
result = list(cfl.nearest(10, maxDistance=0))
self.assertEqual(1, len(result))
self.assertIs(landmark, result[0])
def testFindLandmarkAndTrigPointWithOffsetBiggerThanBoth(self):
"""
If a combined feature list has one landmark and one trig point and the
passed offset is larger than both their offsets, the nearest method
should yield them both (landmarks first, due to landmark priority,
even though it is further away than the trig point).
"""
landmark = Landmark('name1', 'L', 0, 1)
trigPoint = TrigPoint('name2', 'T', 10)
cfl = CombinedFeatureList([landmark], [trigPoint])
result = list(cfl.nearest(20))
self.assertEqual([landmark, trigPoint], result)
def getPairs(self,
limitPerLandmark=None,
maxDistance=None,
minDistance=None):
"""
Get pairs of (landmark, trig point) for use in building a search
dictionary that can be used to identify this read.
When considering each landmark, other landmarks to the left (with
smaller offset) of the current landmark are ignored. This is to
reduce the redundancy that results if both (landmark1, landmark2)
and (landmark2, landmark1) pairs are yielded.
@param limitPerLandmark: An C{int} limit on the number of pairs to
yield per landmark.
@param maxDistance: The C{int} maximum distance permitted between
yielded pairs.
@param minDistance: The C{int} minimum distance permitted between
yielded pairs.
@return: A generator that yields (landmark, trig point) pairs.
"""
if limitPerLandmark is not None and limitPerLandmark < 1:
return
features = CombinedFeatureList(self.landmarks, self.trigPoints)
for landmark in self.landmarks:
count = 0
landmarkOffset = landmark.offset
nearest = features.nearest(landmarkOffset,
maxDistance=maxDistance,
minDistance=minDistance)
while limitPerLandmark is None or count < limitPerLandmark:
try:
feature = next(nearest)
except StopIteration:
break
else:
# Yield any landmark or trig point on the right (with
# greater offset) of the current landmark, and all trig
# points (whether left or right).
if (feature.offset > landmarkOffset
or isinstance(feature, TrigPoint)):
yield landmark, feature
count += 1
def testFindManyMinDistanceMaxDistance(self):
"""
If a combined feature list has many landmarks and trig points, some
outside the minDistance, some outside the maxDistance, find the right
ones.
"""
landmark1 = Landmark('name1', 'L1', 0, 1)
landmark2 = Landmark('name2', 'L2', 3, 1)
landmark3 = Landmark('name3', 'L3', 5, 1)
landmark4 = Landmark('name4', 'L4', 7, 1)
trigPoint1 = TrigPoint('name5', 'T1', 9)
trigPoint2 = TrigPoint('name6', 'T2', 11)
trigPoint3 = TrigPoint('name7', 'T3', 13)
cfl = CombinedFeatureList([landmark1, landmark2, landmark3, landmark4],
[trigPoint1, trigPoint2, trigPoint3])
result = list(cfl.nearest(0, maxDistance=10, minDistance=4))
self.assertEqual([landmark3, landmark4, trigPoint1], result)
def testFindMany(self):
"""
If a combined feature list has many landmarks and trig points
the nearest method should yield them all.
"""
landmark1 = Landmark('name1', 'L1', 0, 1)
landmark2 = Landmark('name2', 'L2', 3, 1)
landmark3 = Landmark('name3', 'L3', 5, 1)
landmark4 = Landmark('name4', 'L4', 7, 1)
trigPoint1 = TrigPoint('name5', 'T1', 9)
trigPoint2 = TrigPoint('name6', 'T2', 11)
trigPoint3 = TrigPoint('name7', 'T3', 13)
cfl = CombinedFeatureList([landmark1, landmark2, landmark3, landmark4],
[trigPoint1, trigPoint2, trigPoint3])
result = list(cfl.nearest(0))
self.assertEqual([
landmark1, landmark2, landmark3, landmark4, trigPoint1, trigPoint2,
trigPoint3
], result)