def test_indexfind_gt():
sl = SortedList([3, 6, 1, 7, 0])
assert (sl.index_gt(3) == 3)
assert (sl.find_gt(3) == 6)
with pytest.raises(ValueError):
sl.index_gt(7)
with pytest.raises(ValueError):
sl.find_gt(7)
def test_indexfind_gt():
sl = SortedList([3, 6, 1, 7, 0])
assert(sl.index_gt(3) == 3)
assert(sl.find_gt(3) == 6)
with pytest.raises(ValueError):
sl.index_gt(7)
with pytest.raises(ValueError):
sl.find_gt(7)
class SegmentAnnotation(collections.Sequence):
"""
Annotation for contiguous time segment.
This class represents a contiguous sequence of annotations. It contains
methods for efficiently finding the annotation corresponding to a temporal
interval.
Parameters
----------
name : string
Identifier for the annotation.
tokens : list of Fragment objects
The sequence of annotations.
Attributes
----------
interval : Interval
The temporal interval that is covered.
Raises
------
ValueError
If tokens are not contiguous or don't all have the same name.
"""
def __init__(self, name, tokens):
self.name = name
self.tokens = SortedList(tokens, key=cmp_to_key(token_cmp))
if len(self.tokens) == 0:
self.interval = None
else:
self.interval = Interval(self.tokens[0].interval.start,
self.tokens[-1].interval.end)
if not all(t1.interval.end == t2.interval.start
for t1, t2 in zip(self.tokens[:-1], self.tokens[1:])):
raise ValueError('Non-contiguous tokens.')
def __len__(self):
return len(self.tokens)
def __iter__(self):
return iter(self.tokens)
def __getitem__(self, i):
return self.tokens[i]
def __repr__(self):
return '%s(%r)' % (self.__class__.__name__, self.__dict__)
def __str__(self):
return '<SegmentAnnotation {0} {1} {2} tokens>'.format(
self.name, str(self.interval), len(self.tokens))
def __eq__(self, other):
if self.name != other.name:
return False
if self.interval != other.interval:
return False
if len(self.tokens) != len(other.tokens):
return False
return all(t1 == t2 for t1, t2 in zip(self.tokens, other.tokens))
def __ne__(self, other):
return not self.__eq__(other)
def restrict(self, interval_db):
"""
Restrict the SegmentAnnotation to a set of Intervals.
Returns a new SegmentAnnotation object with only the FragmentTokens
that are fully covered in `interval_db`.
Parameters
----------
interval_db : IntervalDB
Returns
-------
SegmentAnnotation
New SegmentAnnotation object.
"""
return SegmentAnnotation(self.name,
[f for f in self.tokens
if interval_db.is_covered(f.name, f.interval)])
def annotation_at_interval(self, interval):
"""
Get the annotation corresponding to an interval.
Parameters
----------
interval : Interval
Returns
-------
s : list of strings
Annotation symbols covered by the interval.
"""
return tuple([x.mark for x in self.tokens_at_interval(interval)])
def tokens_at_interval(self, interval):
"""
Get the annotation tokens corresponding to an interval.
Parameters
----------
interval : Interval
Returns
-------
tuple of FragmentTokens
FragmentTokens covered by the interval.
"""
if len(self.tokens) > 0:
name = self.tokens[0].name
else:
return tuple()
dummy_token = FragmentToken(name, interval, None)
try:
start = self.tokens.index_ge(dummy_token)
except ValueError:
return tuple()
try:
stop = self.tokens.index_gt(dummy_token)
except ValueError:
stop = len(self.tokens)
return tuple([x for x in self.tokens[start:stop]])
class SegmentAnnotation(collections.Sequence):
"""
Annotation for contiguous time segment.
This class represents a contiguous sequence of annotations. It contains
methods for efficiently finding the annotation corresponding to a temporal
interval.
Parameters
----------
name : string
Identifier for the annotation.
tokens : list of Fragment objects
The sequence of annotations.
Attributes
----------
interval : Interval
The temporal interval that is covered.
Raises
------
ValueError
If tokens are not contiguous or don't all have the same name.
"""
def __init__(self, name, tokens):
self.name = name
self.tokens = SortedList(tokens, key=cmp_to_key(token_cmp))
if len(self.tokens) == 0:
self.interval = None
else:
self.interval = Interval(self.tokens[0].interval.start,
self.tokens[-1].interval.end)
if not all(t1.interval.end == t2.interval.start
for t1, t2 in zip(self.tokens[:-1], self.tokens[1:])):
# raise ValueError('Non-contiguous tokens.')
pass
def __len__(self):
return len(self.tokens)
def __iter__(self):
return iter(self.tokens)
def __getitem__(self, i):
return self.tokens[i]
def __repr__(self):
return '%s(%r)' % (self.__class__.__name__, self.__dict__)
def __str__(self):
return '<SegmentAnnotation {0} {1} {2} tokens>'.format(
self.name, str(self.interval), len(self.tokens))
def __eq__(self, other):
if self.name != other.name:
return False
if self.interval != other.interval:
return False
if len(self.tokens) != len(other.tokens):
return False
return all(t1 == t2 for t1, t2 in zip(self.tokens, other.tokens))
def __ne__(self, other):
return not self.__eq__(other)
def restrict(self, interval_db):
"""
Restrict the SegmentAnnotation to a set of Intervals.
Returns a new SegmentAnnotation object with only the FragmentTokens
that are fully covered in `interval_db`.
Parameters
----------
interval_db : IntervalDB
Returns
-------
SegmentAnnotation
New SegmentAnnotation object.
"""
return SegmentAnnotation(self.name,
[f for f in self.tokens
if interval_db.is_covered(f.name, f.interval)])
def annotation_at_interval(self, interval):
"""
Get the annotation corresponding to an interval.
Parameters
----------
interval : Interval
Returns
-------
s : list of strings
Annotation symbols covered by the interval.
"""
return tuple([x.mark for x in self.tokens_at_interval(interval)])
def tokens_at_interval(self, interval):
"""
Get the annotation tokens corresponding to an interval.
Parameters
----------
interval : Interval
Returns
-------
tuple of FragmentTokens
FragmentTokens covered by the interval.
"""
if len(self.tokens) > 0:
name = self.tokens[0].name
else:
return tuple()
dummy_token = FragmentToken(name, interval, None)
try:
start = self.tokens.index_ge(dummy_token)
except ValueError:
return tuple()
try:
stop = self.tokens.index_gt(dummy_token)
except ValueError:
stop = len(self.tokens)
return tuple([x for x in self.tokens[start:stop]])
