def get_module_frames(modules,
module_level=0,
glyph_size=GLYPHSIZE,
space=SPACER,
submodule_origin=None,
has_frame_box=False):
frame_list = []
origins = get_origin_list(modules, module_level, glyph_size, space,
submodule_origin)
for i, module in enumerate(modules):
if len(module.children) != 0.:
frame_list += get_module_frames(
module.children, module_level + 1,
GLYPHSIZE - RECURSE_DECREMENT * 2, space,
[origins[i][0] + 2 * space, origins[i][1] + 1.5 * space], True)
else:
if module.part_list != None:
parts_count = len(module.part_list.parts)
else:
parts_count = 0
width, height = get_module_width_height(parts_count, glyph_size,
space,
len(module.other_parts))
frame_list.append(
rd.Frame(width=width, height=height, origin=origins[i]))
module.level = module_level
if has_frame_box and len(frame_list) != 0.:
frame_list.append(get_biggest_module_frame(frame_list, space))
return frame_list
def get_biggest_module_frame(framelist, space_offset):
max_x, max_y = (np.finfo(np.float128).min for i in range(2))
min_x, min_y = (np.finfo(np.float128).max for i in range(2))
for frame in framelist:
if min_x > frame.origin[0]:
min_x = frame.origin[0]
if max_x < frame.origin[0] + frame.width:
max_x = frame.origin[0] + frame.width
if min_y > frame.origin[1]:
min_y = frame.origin[1]
if max_y < frame.origin[1] + frame.height:
max_y = frame.origin[1] + frame.height
return rd.Frame(
width=(max_x - min_x) + 4 * space_offset,
height=(max_y - min_y) + 3.5 * space_offset,
origin=[min_x - 2 * space_offset, min_y - 1.5 * space_offset])
def draw_module(ax,
module,
module_frame,
glyph_size,
module_spacer,
haveBackbone=True):
glyph_pos = [
module_frame.origin[0] + 3 * module_spacer,
module_frame.origin[1] + 1.5 * module_spacer
]
renderer = rd.GlyphRenderer()
strand_rd = rd.StrandRenderer()
module_rd = rd.ModuleRenderer()
# check whether module is empty or not
if module.part_list == None:
if len(module.children) != 0:
return module_rd.draw_empty_module_box(ax, module_frame)
elif len(module.other_parts) == 0:
return
# draw each glyphs in module part list
else:
module.part_list.position = glyph_pos
for part in module.part_list.parts:
part.frame = rd.Frame(width=glyph_size,
height=glyph_size,
origin=glyph_pos)
child = renderer.draw_glyph(ax, part.type, glyph_pos, glyph_size,
0.)
strand_rd.add_glyphs(child)
module_rd.add_parts(child)
glyph_pos = [
glyph_pos[0] + glyph_size + module_spacer, glyph_pos[1]
]
# draw backbone
if haveBackbone and module.part_list != None:
bb = strand_rd.draw_backbone_strand(ax, glyph_pos[1], module_spacer)
module_rd.add_parts(bb)
module.part_list.position = bb['frame'].origin
# draw other parts
if len(module.other_parts) != 0:
op_pos_list = __get_other_part_pos(len(module.other_parts),
module_frame, glyph_size,
glyph_size, module_spacer)
other_part_frames = []
for i, other_part in enumerate(module.other_parts):
other_part.frame = rd.Frame(width=glyph_size,
height=glyph_size,
origin=op_pos_list[i])
other_part_frames.append(other_part.frame)
other_child = renderer.draw_glyph(ax, other_part.type,
op_pos_list[i], glyph_size, 0.)
module_rd.add_parts(other_child)
# do not draw module frame box if only has other part
if module.part_list == None:
return get_biggest_module_frame(other_part_frames, module_spacer)
return module_rd.draw_module_box(ax, module_spacer, module_spacer)
'''
import render
import matplotlib.pyplot as plt
# default setting
strand = render.StrandRenderer()
renderer = render.GlyphRenderer()
module = render.ModuleRenderer()
print(renderer.glyphs_library)
print('------------')
print(renderer.glyph_soterm_map)
fig = plt.figure(figsize=(5, 5))
ax = fig.add_subplot(111)
# need to set axis first
ax.set_xlim(-50.0, 50.0)
ax.set_ylim(-50.0, 50.0)
p1 = renderer.draw_glyph(ax, 'Promoter', (-20.0, 0.0), 10., 0)
ori2 = renderer.draw_glyph(ax, 'OriginOfReplication', (0.0, -5.), 10., 0)
i3 = renderer.draw_glyph(ax, 'Insulator', (20.0, -5.), 10., 0.)
strand.add_glyphs([p1, ori2, i3])
bb = strand.draw_backbone_strand(ax, 0., 1.5)
module.add_parts([p1, ori2, i3, bb])
module_frame = module.draw_module_box(
ax, render.Frame(width=70, height=30, origin=(-30, -10)))
ax.set_axis_off()
plt.show()
def draw_module(ax,
module,
module_frame,
glyph_size,
module_spacer,
haveBackbone=True,
user_spec=None):
strand_adjustment = __get_strand_adjustment(module.part_list, user_spec,
glyph_size)
glyph_pos = [
module_frame.origin[0] + 3 * module_spacer,
module_frame.origin[1] + 1.5 * module_spacer + strand_adjustment
]
renderer = rd.GlyphRenderer()
strand_rd = rd.StrandRenderer()
module_rd = rd.ModuleRenderer()
# check whether module is empty or not
if module.part_list == None:
if len(module.children) != 0 and len(module.other_parts) == 0:
return module_rd.draw_module_box(ax, module_frame)
# draw each glyphs in module part list
else:
module.part_list.position = glyph_pos
custom_glyph_size = glyph_size
for part in module.part_list.parts:
if part.type in LOWER_ORIGIN_GLYPHS: # adjust for cds etc
glyph_pos[1] -= strand_adjustment
if __check_custom_size(part.name, user_spec,
glyph_size) != glyph_size: # user_param
glyph_size *= __check_custom_size(part.name, user_spec)
#rendering
part.frame = rd.Frame(width=glyph_size,
height=glyph_size,
origin=glyph_pos)
child = renderer.draw_glyph(ax,
part.type,
glyph_pos,
glyph_size,
0.,
user_parameters=__find_right_spec(
part.name, user_spec))
strand_rd.add_glyphs(child)
module_rd.add_parts(child)
# prepare for next part
if part.type in LOWER_ORIGIN_GLYPHS:
glyph_pos[1] += strand_adjustment
glyph_pos = [
glyph_pos[0] + glyph_size + module_spacer, glyph_pos[1]
]
if custom_glyph_size != glyph_size: glyph_size = custom_glyph_size
# draw backbone
if haveBackbone and module.part_list != None:
bb = strand_rd.draw_backbone_strand(ax, glyph_pos[1], module_spacer)
module_rd.add_parts(bb)
module.part_list.position = bb['frame'].origin
# draw other parts
if len(module.other_parts) != 0:
op_pos_list = __get_other_part_pos(len(module.other_parts),
module_frame, glyph_size,
glyph_size, module_spacer)
other_part_frames = []
for i, other_part in enumerate(module.other_parts):
other_part.frame = rd.Frame(width=glyph_size,
height=glyph_size,
origin=op_pos_list[i])
other_part_frames.append(other_part.frame)
other_child = renderer.draw_glyph(
ax,
other_part.type,
op_pos_list[i],
glyph_size,
user_parameters=__find_right_spec(other_part.name, user_spec))
module_rd.add_parts(other_child)
return module_rd.draw_module_box(ax, module_frame)