def getRegionCoveringAll(self, annotations):
spans = []
annotation_types = []
for annot in annotations:
spans.extend(annot.map.spans)
if annot.type not in annotation_types:
annotation_types.append(annot.type)
map = Map(spans=spans, parent_length=len(self))
map = map.covered() # No overlaps
Name = ','.join(annotation_types)
return _Feature(self, map, type='region', Name=Name)
def getRegionCoveringAll(self, annotations):
spans = []
annotation_types = []
for annot in annotations:
spans.extend(annot.map.spans)
if annot.type not in annotation_types:
annotation_types.append(annot.type)
map = Map(spans=spans, parent_length=len(self))
map = map.covered() # No overlaps
Name = ','.join(annotation_types)
return _Feature(self, map, type='region', Name=Name)
def Feature(parent, type, Name, spans, value=None):
if isinstance(spans, Map):
map = spans
assert map.parent_length == len(parent), (map, len(parent))
else:
map = Map(locations=spans, parent_length=len(parent))
return AnnotatableFeature(parent, map, type=type, Name=Name)
def _shiftedAnnotations(self, new, shift):
result = []
if self.annotations:
newmap = Map([(shift, shift + len(self))], parent_length=len(new))
for annot in self.annotations:
annot = annot.remappedTo(new, newmap)
result.append(annot)
return result
def Variable(parent, type, Name, xxy_list):
"""A variable that has 2 x-components (start, end) and a single y component.
Currently used by Vestige - BMC Bioinformatics, 6:130, 2005."""
start = min([min(x1, x2) for ((x1, x2), y) in xxy_list])
end = max([max(x1, x2) for ((x1, x2), y) in xxy_list])
if start != 0:
xxy_list = [((x1-start, x2-start), y) for ((x1, x2), y) in xxy_list]
end -= start
#values = [location.Span(x1-start, x2-start, True, True, y) for ((x1, x2), y) in xxy]
map = Map([(start, end)], parent_length=len(parent))
return _Variable(parent, map, type=type, Name=Name, xxy_list=xxy_list)
def _as_map(self, index):
"""Can take a slice, integer, map or feature, or even a list/tuple of those"""
if type(index) in [list, tuple]:
spans = []
for i in index:
spans.extend(self._as_map(i).spans)
map = Map(spans=spans, parent_length=len(self))
elif isinstance(index, _Feature):
feature = index
map = feature.map
base = feature.parent
containers = []
while feature and base is not self and hasattr(base, 'parent'):
containers.append(base)
base = base.parent
if base is not self:
raise ValueError("Can't map %s onto %s via %s" % (index, repr(self), containers))
for base in containers:
feature = feature.remappedTo(base, base.map)
index = map
else:
map = as_map(index, len(self))
return map
def SimpleVariable(parent, type, Name, data):
"""A simple variable type of annotation, such as a computed property of
a sequence that varies spatially."""
assert len(data) == len(parent), (len(data), len(parent))
map = Map([(0, len(data))], parent_length=len(parent))
return _SimpleVariable(parent, map, type=type, Name=Name, data=data)