def save_part_as_component_definition(docu, md, part, part_type):
part_rd = rd.GlyphRenderer()
comp = sbol.ComponentDefinition(part.name, sbol.BIOPAX_DNA)
if part_type != sbol.BIOPAX_RNA:
comp.roles = part_rd.get_so_term(part_type)
func_comp = md.functionalComponents.create(comp.displayId)
func_comp.definition = comp
save_frame_into_file(comp, part.frame.width, part.frame.height,
part.frame.origin[0], part.frame.origin[1])
docu.addComponentDefinition(comp)
def main():
print('executed')
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)
strand = render.StrandRenderer()
renderer = render.GlyphRenderer()
p1 = renderer.draw_glyph(ax, 'Promoter', (-20.0, 0.0), 5., 0)
i3 = renderer.draw_glyph(ax, 'Insulator', (20.0, -2.5), 5., 0.)
strand.add_glyphs([p1, i3])
strand.draw_backbone_strand(ax, 0.0, 2)
ax.set_axis_off()
plt.show()
def add_parts_to_module(mod, raw_md, d):
renderer = rd.GlyphRenderer()
for fc in raw_md.functionalComponents:
c = d.componentDefinitions[fc.displayId]
# create part
if sbol.BIOPAX_DNA in c.types:
part = dt.Part(mod, fc.displayId,
renderer.glyph_soterm_map.get(c.roles[0]))
mod.add_strand_part(part)
else:
if sbol.BIOPAX_RNA in c.types:
part = dt.Part(mod, fc.displayId, 'RNA')
elif sbol.BIOPAX_PROTEIN in c.types:
part = dt.Part(mod, fc.displayId, 'Macromolecule')
else:
part = dt.Part(mod, fc.displayId, 'Unspecified')
mod.add_non_strand_part(part)
return mod
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)
'''
rough script for rendering three glyphs onto one module
need to be moved outside the example directory
at the same directory as render.py
'''
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(
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)