def draw_annotation_maps(seq, annot_maps,
default_colors=None,
picture_class=BitmapSequencePicture,
wrappers=None):
# make sure the list of default colors is the same length as the list
# of input annotation maps.
if default_colors is None:
default_colors = [ 'black' ] * len(annot_maps)
else:
default_colors = list(default_colors)
for i in range(len(default_colors), len(annot_maps)):
default_colors.append('black')
# make sure the list of feature wrappers is the same length as the
# list of input annotation maps.
if wrappers is None:
wrappers = [ None ] * len(annot_maps)
else:
wrappers = list(wrappers)
for i in range(len(wrappers), len(annot_maps)):
wrappers.append(None)
# create an instance of the picture class, whatever it may be.
p = picture_class(len(seq))
### underneath, draw each set of annotations
l = []
maxmax_text_length = 0
for n, annot_map in enumerate(annot_maps):
default_color = default_colors[n]
try:
annots = annot_map[seq]
except (KeyError, TypeError): # sequence not in map, or map is None
continue
new_map, max_text_length = \
convert_to_image_coords(seq, annots, p, default_color,
wrappers[n])
if new_map:
l.append(new_map)
maxmax_text_length = max(maxmax_text_length, max_text_length)
p.set_left_margin_offset(maxmax_text_length)
### draw the basic sequence line
p.draw_sequence_line()
start_slot = 0
for new_map in l:
n_slots = p.draw_annotations(new_map, start_slot=start_slot)
start_slot += n_slots
return p
def draw(self, seq):
picture = draw_annotation_maps(seq, self.maps,
default_colors=self.default_colors,
picture_class=self.picture_class,
wrappers=self.wrappers)
return picture
# def draw_annotation_maps(seq, annot_maps,
# default_colors=None,
# picture_class=None,
# wrappers=None):
annot_maps = self.maps
default_colors=self.default_colors
picture_class=self.picture_class
wrappers=self.wrappers
if picture_class is None:
picture_class = get_picture_class
# make sure the list of default colors is the same length as the list
# of input annotation maps.
if default_colors is None:
default_colors = [ 'black' ] * len(annot_maps)
else:
default_colors = list(default_colors)
for i in range(len(default_colors), len(annot_maps)):
default_colors.append('black')
# make sure the list of feature wrappers is the same length as the
# list of input annotation maps.
if wrappers is None:
wrappers = [ None ] * len(annot_maps)
else:
wrappers = list(wrappers)
for i in range(len(wrappers), len(annot_maps)):
wrappers.append(None)
# create an instance of the picture class, whatever it may be.
p = picture_class(seq)
self.p = p
### underneath, draw each set of annotations
l = []
maxmax_text_length = 0 # keep track of left margin offset
for n, annot_map in enumerate(annot_maps):
default_color = default_colors[n]
if isinstance(annot_map, SpanMap):
try:
annot_map.nlmsa[seq]
l.append(annot_map)
except KeyError:
pass
# either way, no further processing needed
continue
try:
annots = annot_map[seq]
except (KeyError, TypeError): # sequence not in map, or map is None
continue
new_map, max_text_length = \
convert_to_image_coords(seq, annots, p, default_color,
wrappers[n])
if new_map:
l.append(new_map)
maxmax_text_length = max(maxmax_text_length, max_text_length)
p.set_left_margin_offset(maxmax_text_length)
### draw the basic sequence line
p.draw_sequence_line()
start_slot = 0
for new_map in l:
if isinstance(new_map, SpanMap):
color = None
if new_map.line_color:
color = getattr(p.colors, new_map.line_color)
fill = None
if new_map.fill_color:
fill = getattr(p.colors, new_map.fill_color)
pairs = new_map.transform_coords_to_picture(seq, p)
n_slots = p._draw_xy_plot(start_slot,
seq.start, seq.stop,
pairs, new_map.height,
color=color, fill=fill)
n_slots = new_map.height
else:
n_slots = p.draw_annotations(new_map, start_slot=start_slot)
start_slot += n_slots
###
return p