def comp_to_meta_node(meta_graph, c_id, go_id, c_name, out_comp, do_layout=True, n2xy=None):
root = meta_graph.getRoot()
ns = [n for n in meta_graph.getNodes() if root[COMPARTMENT_ID][n] == c_id]
if not ns:
return None
comp_n = meta_graph.createMetaNode(ns, False)
comp_graph = root[VIEW_META_GRAPH][comp_n]
if do_layout:
if n2xy:
apply_node_coordinates(comp_graph, n2xy)
else:
layout(comp_graph)
root[NAME][comp_n] = c_name
root[COMPARTMENT_ID][comp_n] = out_comp
root[TYPE][comp_n] = TYPE_COMPARTMENT
root[VIEW_SHAPE][comp_n] = COMPARTMENT_SHAPE
root[ID][comp_n] = c_id
root[TERM][comp_n] = go_id
root[VIEW_SIZE][comp_n] = get_n_size(meta_graph, comp_n)
for meta_e in root.getInOutEdges(comp_n):
sample_e = next((ee for ee in root[VIEW_META_GRAPH][meta_e] if not root[UBIQUITOUS][ee]),
next(iter(root[VIEW_META_GRAPH][meta_e])))
root[UBIQUITOUS][meta_e] = root[UBIQUITOUS][sample_e]
root[STOICHIOMETRY][meta_e] = sum(root[STOICHIOMETRY][ee] for ee in root[VIEW_META_GRAPH][meta_e])
# todo: this is not True but will help with cycle detection
root[REVERSIBLE][meta_e] = root[REVERSIBLE][sample_e] and not root[UBIQUITOUS][sample_e]
return comp_n
def process_compartments(c_id2info, meta_graph, n2xy=None):
# root = meta_graph.getRoot()
factor_nodes(meta_graph)
current_zoom_level = max({info[2][0] for info in c_id2info.values()})
while current_zoom_level >= 0:
for c_id in c_id2info.keys():
(name, go, (l, out_c_id)) = c_id2info[c_id]
if current_zoom_level == l:
# ns = [n for n in meta_graph.getNodes() if root[COMPARTMENT_ID][n] == c_id]
# factor_nodes(meta_graph, ns)
comp_to_meta_node(meta_graph, c_id, go, name, out_c_id, True, n2xy)
current_zoom_level -= 1
if n2xy:
apply_node_coordinates(meta_graph, n2xy)
else:
layout(meta_graph)
def process_compartments(c_id2info, meta_graph, n2xy=None):
# root = meta_graph.getRoot()
factor_nodes(meta_graph)
current_zoom_level = max({info[2][0] for info in c_id2info.values()})
while current_zoom_level >= 0:
for c_id in c_id2info.keys():
(name, go, (l, out_c_id)) = c_id2info[c_id]
if current_zoom_level == l:
# ns = [n for n in meta_graph.getNodes() if root[COMPARTMENT_ID][n] == c_id]
# factor_nodes(meta_graph, ns)
comp_to_meta_node(meta_graph, c_id, go, name, out_c_id, True,
n2xy)
current_zoom_level -= 1
if n2xy:
apply_node_coordinates(meta_graph, n2xy)
else:
layout(meta_graph)