def _get_is_simple(self, anchor, context, syn):
# are all the intervals on the same contig?
all_on_same_contig = intervals.allequal((x.over.contig for x in context))
# make an interval describing the start and stop of the query context
qminstart = min(x.start for x in context)
qmaxstop = max(x.stop for x in context)
tminstart = min(x.over.start for x in context)
tmaxstop = max(x.over.stop for x in context)
query_bound = intervals.Interval(contig=anchor.contig, start=qminstart, stop=qmaxstop)
target_bound = intervals.Interval(contig=anchor.over.contig, start=tminstart, stop=tmaxstop)
has_outer = False
for q in syn.target.get_overlapping(target_bound):
if not intervals.overlaps(query_bound, q.over):
has_outer = True
break
is_simple = all_on_same_contig and not has_outer
return(is_simple)
def test_allequal(self):
self.assertTrue(intervals.allequal([1,1,1,1]))
self.assertTrue(intervals.allequal(['a', 'a', 'a', 'a']))
