def fill_chromosome(self, chromosome):
"""Add the collected segment information to a chromosome for drawing.
Arguments:
- chromosome - A Chromosome graphics object that we can add
chromosome segments to.
This creates ChromosomeSegment (and TelomereSegment) objects to
fill in the chromosome. The information is derived from the
label and count information, with counts transformed to the
specified color map.
Returns the chromosome with all of the segments added.
"""
for seg_num in range(len(self._names)):
is_end_segment = 0
# make the top and bottom telomeres
if seg_num == 0:
cur_segment = TelomereSegment()
is_end_segment = 1
elif seg_num == len(self._names) - 1:
cur_segment = TelomereSegment(1)
is_end_segment = 1
# otherwise, they are just regular segments
else:
cur_segment = ChromosomeSegment()
seg_name = self._names[seg_num]
if self._count_info[seg_name] > 0:
color = self._color_from_count(self._count_info[seg_name])
cur_segment.fill_color = color
if self._label_info[seg_name] is not None:
cur_segment.label = self._label_info[seg_name]
# give end segments extra size so they look right
if is_end_segment:
cur_segment.scale = 3
else:
cur_segment.scale = self._scale_info[seg_name]
chromosome.add(cur_segment)
return chromosome
def fill_chromosome(self, chromosome):
"""Add the collected segment information to a chromosome for drawing.
Arguments:
o chromosome - A Chromosome graphics object that we can add
chromosome segments to.
This creates ChromosomeSegment (and TelomereSegment) objects to
fill in the chromosome. The information is derived from the
label and count information, with counts transformed to the
specified color map.
Returns the chromosome with all of the segments added.
"""
for seg_num in range(len(self._names)):
is_end_segment = 0
# make the top and bottom telomeres
if seg_num == 0:
cur_segment = TelomereSegment()
is_end_segment = 1
elif seg_num == len(self._names) - 1:
cur_segment = TelomereSegment(1)
is_end_segment = 1
# otherwise, they are just regular segments
else:
cur_segment = ChromosomeSegment()
seg_name = self._names[seg_num]
if self._count_info[seg_name] > 0:
color = self._color_from_count(self._count_info[seg_name])
cur_segment.fill_color = color
if self._label_info[seg_name] is not None:
cur_segment.label = self._label_info[seg_name]
# give end segments extra size so they look right
if is_end_segment:
cur_segment.scale = 3
else:
cur_segment.scale = self._scale_info[seg_name]
chromosome.add(cur_segment)
return chromosome
