def layout_outer_elements(graph):
root = graph.getRoot()
comps = [c for c in graph.getNodes() if TYPE_COMPARTMENT == root[TYPE][c]]
for c in comps:
c_left_x, c_bottom_y, c_right_x, c_top_y = get_comp_borders(c, root)
c_w, c_h = (c_right_x - c_left_x) / 2, (c_top_y - c_bottom_y) / 2
rs = sorted([r for r in graph.getInOutNodes(c)
if len([s for s in graph.getInOutNodes(r) if not ub_or_single(s, graph)]) == 1],
key=lambda r: -get_n_length(root, r))
comp_mg = root[VIEW_META_GRAPH][c]
min_inner_node_x = min(root[VIEW_LAYOUT][s].getX() - root[VIEW_SIZE][s].getW() / 2 for s in comp_mg.getNodes())
min_inner_node_y = min(root[VIEW_LAYOUT][s].getY() - root[VIEW_SIZE][s].getH() / 2 for s in comp_mg.getNodes())
coords = set()
h_jump, v_jump = True, True
for r in rs:
r_w, r_h = root[VIEW_SIZE][r].getW() * 3, root[VIEW_SIZE][r].getH() * 3
inner_r_metabolite_ns = [s for s in root.getInOutNodes(r) if comp_mg.isElement(s)]
inner_r_metabolite_ns_not_ub = [s for s in inner_r_metabolite_ns if not ub_or_single(s, comp_mg)]
if inner_r_metabolite_ns_not_ub:
inner_r_metabolite_ns = inner_r_metabolite_ns_not_ub
else:
inner_r_metabolite_ns_not_ub = [s for s in inner_r_metabolite_ns if not root[UBIQUITOUS][s]]
if inner_r_metabolite_ns_not_ub:
inner_r_metabolite_ns = inner_r_metabolite_ns_not_ub
avg_inner_r_metabolite_x, avg_inner_r_metabolite_y = \
sum(root[VIEW_LAYOUT][s].getX() - min_inner_node_x for s in inner_r_metabolite_ns) / len(inner_r_metabolite_ns), \
sum(root[VIEW_LAYOUT][s].getY() - min_inner_node_y for s in inner_r_metabolite_ns) / len(inner_r_metabolite_ns)
x = c_left_x - r_w if avg_inner_r_metabolite_x < c_w else c_right_x + r_h
y = c_bottom_y - r_h if avg_inner_r_metabolite_y < c_h else c_top_y + r_h
# if we are closer to the compartment from bottom or top rather than from left or right
if abs(c_left_x + avg_inner_r_metabolite_x - x) > abs(c_bottom_y + avg_inner_r_metabolite_y - y):
# stay below/above of the inner metabolites
r_x = c_left_x + avg_inner_r_metabolite_x
r_y = y
while (r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE) in coords:
r_x += 3 * r_w if avg_inner_r_metabolite_x < c_w else -3 * r_w
if v_jump:
r_y -= r_h if avg_inner_r_metabolite_y < c_h else r_h
v_jump = not v_jump
# we are closer to the compartment from left or right rather than from bottom or top
else:
# stay to the left/right of the inner metabolites
r_y = c_bottom_y + avg_inner_r_metabolite_y
r_x = x
while (r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE) in coords:
r_y += 3 * r_h if avg_inner_r_metabolite_y < c_h else -3 * r_h
if h_jump:
r_x -= r_w if avg_inner_r_metabolite_x < c_w else r_w
h_jump = not h_jump
coords.add((r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE))
root[VIEW_LAYOUT][r] = tlp.Coord(r_x, r_y)
def layout_inner_elements(graph, c_id, c_left_x, c_bottom_y, c_right_x,
c_top_y):
root = graph.getRoot()
neighbours_outside_comp = lambda r: [
n for n in graph.getInOutNodes(r) if root[COMPARTMENT_ID][n] != c_id
]
neighbours_inside_comp = lambda r: [
n for n in graph.getInOutNodes(r)
if root[COMPARTMENT_ID][n] == c_id and not ub_or_single(n, graph)
]
rs = sorted([
r for r in graph.getNodes() if root[COMPARTMENT_ID][r] == c_id
and not neighbours_inside_comp(r) and neighbours_outside_comp(r)
],
key=lambda r: -get_n_length(root, r))
coords = set()
h_jump, v_jump = True, True
for r in rs:
r_w, r_h = root[VIEW_SIZE][r].getW(), root[VIEW_SIZE][r].getH()
outside_r_metabolites = neighbours_outside_comp(r)
outside_r_metabolites_not_ub = [
s for s in outside_r_metabolites if not ub_or_single(s, graph)
]
if outside_r_metabolites_not_ub:
outside_r_metabolites = outside_r_metabolites_not_ub
avg_outside_r_metabolite_x, avg_outside_r_metabolite_y = \
sum(root[VIEW_LAYOUT][s].getX() for s in outside_r_metabolites) / len(outside_r_metabolites), \
sum(root[VIEW_LAYOUT][s].getY() for s in outside_r_metabolites) / len(outside_r_metabolites)
inside_y = c_bottom_y + r_h <= avg_outside_r_metabolite_y <= c_top_y - r_h
inside_x = c_left_x + r_w <= avg_outside_r_metabolite_x <= c_right_x - r_w
closer_to_the_compartment_bottom = \
abs(avg_outside_r_metabolite_y - c_bottom_y) < abs(avg_outside_r_metabolite_y - c_top_y)
closer_to_the_left_comp_border = \
abs(avg_outside_r_metabolite_x - c_left_x) < abs(avg_outside_r_metabolite_x - c_right_x)
if inside_x:
# stay above/below outside metabolites
r_x = avg_outside_r_metabolite_x
r_y = c_bottom_y + r_h if closer_to_the_compartment_bottom else c_top_y - r_h
while (r_x - r_x % REACTION_SIZE,
r_y - r_y % REACTION_SIZE) in coords:
if closer_to_the_left_comp_border:
r_x += 3 * r_w
else:
r_x -= 3 * r_w
if v_jump:
r_y += -r_w if closer_to_the_compartment_bottom else r_w
v_jump = not v_jump
elif inside_y:
# stay to the left/right of the outside metabolites
r_y = avg_outside_r_metabolite_y
r_x = c_left_x + r_w if closer_to_the_left_comp_border else c_right_x - r_w
while (r_x - r_x % REACTION_SIZE,
r_y - r_y % REACTION_SIZE) in coords:
if closer_to_the_compartment_bottom:
r_y += 3 * r_h
else:
r_y -= 3 * r_h
if h_jump:
r_x += -r_h if closer_to_the_left_comp_border else r_h
h_jump = not h_jump
else:
i = 1
while True:
r_x = max(c_left_x + i * r_w,
min(avg_outside_r_metabolite_x, c_right_x - i * r_w))
r_y = max(c_bottom_y + i * r_h,
min(avg_outside_r_metabolite_y, c_top_y - i * r_h))
if (r_x - r_x % REACTION_SIZE,
r_y - r_y % REACTION_SIZE) in coords:
i += 1
else:
break
coords.add((r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE))
root[VIEW_LAYOUT][r] = tlp.Coord(r_x, r_y)
layout_ub_sps(graph, rs, c_id)
# open_meta_ns(graph, (r for r in graph.getNodes() if root[FAKE][r]))
root[VIEW_LAYOUT].setAllEdgeValue([])
def layout_outer_elements(graph):
root = graph.getRoot()
comps = [c for c in graph.getNodes() if TYPE_COMPARTMENT == root[TYPE][c]]
for c in comps:
c_left_x, c_bottom_y, c_right_x, c_top_y = get_comp_borders(c, root)
c_w, c_h = (c_right_x - c_left_x) / 2, (c_top_y - c_bottom_y) / 2
rs = sorted([
r for r in graph.getInOutNodes(c) if len([
s
for s in graph.getInOutNodes(r) if not ub_or_single(s, graph)
]) == 1
],
key=lambda r: -get_n_length(root, r))
comp_mg = root[VIEW_META_GRAPH][c]
min_inner_node_x = min(root[VIEW_LAYOUT][s].getX() -
root[VIEW_SIZE][s].getW() / 2
for s in comp_mg.getNodes())
min_inner_node_y = min(root[VIEW_LAYOUT][s].getY() -
root[VIEW_SIZE][s].getH() / 2
for s in comp_mg.getNodes())
coords = set()
h_jump, v_jump = True, True
for r in rs:
r_w, r_h = root[VIEW_SIZE][r].getW() * 3, root[VIEW_SIZE][r].getH(
) * 3
inner_r_metabolite_ns = [
s for s in root.getInOutNodes(r) if comp_mg.isElement(s)
]
inner_r_metabolite_ns_not_ub = [
s for s in inner_r_metabolite_ns
if not ub_or_single(s, comp_mg)
]
if inner_r_metabolite_ns_not_ub:
inner_r_metabolite_ns = inner_r_metabolite_ns_not_ub
else:
inner_r_metabolite_ns_not_ub = [
s for s in inner_r_metabolite_ns if not root[UBIQUITOUS][s]
]
if inner_r_metabolite_ns_not_ub:
inner_r_metabolite_ns = inner_r_metabolite_ns_not_ub
avg_inner_r_metabolite_x, avg_inner_r_metabolite_y = \
sum(root[VIEW_LAYOUT][s].getX() - min_inner_node_x for s in inner_r_metabolite_ns) / len(inner_r_metabolite_ns), \
sum(root[VIEW_LAYOUT][s].getY() - min_inner_node_y for s in inner_r_metabolite_ns) / len(inner_r_metabolite_ns)
x = c_left_x - r_w if avg_inner_r_metabolite_x < c_w else c_right_x + r_h
y = c_bottom_y - r_h if avg_inner_r_metabolite_y < c_h else c_top_y + r_h
# if we are closer to the compartment from bottom or top rather than from left or right
if abs(c_left_x + avg_inner_r_metabolite_x -
x) > abs(c_bottom_y + avg_inner_r_metabolite_y - y):
# stay below/above of the inner metabolites
r_x = c_left_x + avg_inner_r_metabolite_x
r_y = y
while (r_x - r_x % REACTION_SIZE,
r_y - r_y % REACTION_SIZE) in coords:
r_x += 3 * r_w if avg_inner_r_metabolite_x < c_w else -3 * r_w
if v_jump:
r_y -= r_h if avg_inner_r_metabolite_y < c_h else r_h
v_jump = not v_jump
# we are closer to the compartment from left or right rather than from bottom or top
else:
# stay to the left/right of the inner metabolites
r_y = c_bottom_y + avg_inner_r_metabolite_y
r_x = x
while (r_x - r_x % REACTION_SIZE,
r_y - r_y % REACTION_SIZE) in coords:
r_y += 3 * r_h if avg_inner_r_metabolite_y < c_h else -3 * r_h
if h_jump:
r_x -= r_w if avg_inner_r_metabolite_x < c_w else r_w
h_jump = not h_jump
coords.add((r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE))
root[VIEW_LAYOUT][r] = tlp.Coord(r_x, r_y)
def layout_inner_elements(graph, c_id, c_left_x, c_bottom_y, c_right_x, c_top_y):
root = graph.getRoot()
neighbours_outside_comp = lambda r: [n for n in graph.getInOutNodes(r) if root[COMPARTMENT_ID][n] != c_id]
neighbours_inside_comp = lambda r: [n for n in graph.getInOutNodes(r) if root[COMPARTMENT_ID][n] == c_id
and not ub_or_single(n, graph)]
rs = sorted([r for r in graph.getNodes() if root[COMPARTMENT_ID][r] == c_id and not neighbours_inside_comp(r)
and neighbours_outside_comp(r)], key=lambda r: -get_n_length(root, r))
coords = set()
h_jump, v_jump = True, True
for r in rs:
r_w, r_h = root[VIEW_SIZE][r].getW(), root[VIEW_SIZE][r].getH()
outside_r_metabolites = neighbours_outside_comp(r)
outside_r_metabolites_not_ub = [s for s in outside_r_metabolites if not ub_or_single(s, graph)]
if outside_r_metabolites_not_ub:
outside_r_metabolites = outside_r_metabolites_not_ub
avg_outside_r_metabolite_x, avg_outside_r_metabolite_y = \
sum(root[VIEW_LAYOUT][s].getX() for s in outside_r_metabolites) / len(outside_r_metabolites), \
sum(root[VIEW_LAYOUT][s].getY() for s in outside_r_metabolites) / len(outside_r_metabolites)
inside_y = c_bottom_y + r_h <= avg_outside_r_metabolite_y <= c_top_y - r_h
inside_x = c_left_x + r_w <= avg_outside_r_metabolite_x <= c_right_x - r_w
closer_to_the_compartment_bottom = \
abs(avg_outside_r_metabolite_y - c_bottom_y) < abs(avg_outside_r_metabolite_y - c_top_y)
closer_to_the_left_comp_border = \
abs(avg_outside_r_metabolite_x - c_left_x) < abs(avg_outside_r_metabolite_x - c_right_x)
if inside_x:
# stay above/below outside metabolites
r_x = avg_outside_r_metabolite_x
r_y = c_bottom_y + r_h if closer_to_the_compartment_bottom else c_top_y - r_h
while (r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE) in coords:
if closer_to_the_left_comp_border:
r_x += 3 * r_w
else:
r_x -= 3 * r_w
if v_jump:
r_y += -r_w if closer_to_the_compartment_bottom else r_w
v_jump = not v_jump
elif inside_y:
# stay to the left/right of the outside metabolites
r_y = avg_outside_r_metabolite_y
r_x = c_left_x + r_w if closer_to_the_left_comp_border else c_right_x - r_w
while (r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE) in coords:
if closer_to_the_compartment_bottom:
r_y += 3 * r_h
else:
r_y -= 3 * r_h
if h_jump:
r_x += -r_h if closer_to_the_left_comp_border else r_h
h_jump = not h_jump
else:
i = 1
while True:
r_x = max(c_left_x + i * r_w, min(avg_outside_r_metabolite_x, c_right_x - i * r_w))
r_y = max(c_bottom_y + i * r_h, min(avg_outside_r_metabolite_y, c_top_y - i * r_h))
if (r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE) in coords:
i += 1
else:
break
coords.add((r_x - r_x % REACTION_SIZE, r_y - r_y % REACTION_SIZE))
root[VIEW_LAYOUT][r] = tlp.Coord(r_x, r_y)
layout_ub_sps(graph, rs, c_id)
# open_meta_ns(graph, (r for r in graph.getNodes() if root[FAKE][r]))
root[VIEW_LAYOUT].setAllEdgeValue([])
