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 meta_graph2features(c_id2info, c_id2outs, meta_graph, r2rs_ps, n2xy=None, id2mask=None, onto=None):
root = meta_graph.getRoot()
c_id2level2features = {}
processed = set()
c_id2c_borders = {}
n2layout, e2layout = {}, {}
all_c_id2c_borders = {}
while True:
for c_id, sizes in c_id2c_borders.items():
layout_inner_elements(meta_graph, c_id, *sizes)
if n2xy:
apply_node_coordinates(meta_graph, n2xy)
bend_edges(meta_graph)
straighten_edges_inside_compartments(meta_graph, all_c_id2c_borders)
# bend_edges_around_compartments(meta_graph, (e for e in meta_graph.getEdges() if not get_e_id(e) in processed))
# bend_species_edges(meta_graph)
color_edges(meta_graph)
export_elements(c_id2info, c_id2outs, c_id2level2features, meta_graph, processed, r2rs_ps, n2layout, e2layout,
id2mask=id2mask, onto=onto)
metas = [n for n in meta_graph.getNodes() if meta_graph.isMetaNode(n) and TYPE_COMPARTMENT == root[TYPE][n]]
if not metas:
c_id2c_borders = {}
metas = [n for n in meta_graph.getNodes() if meta_graph.isMetaNode(n)]
if not metas:
break
align_generalized_ns(meta_graph)
rotate_generalized_ns(meta_graph)
bend_ubiquitous_edges(meta_graph, metas)
else:
c_id2c_borders = {root[ID][c]: get_comp_borders(c, root) for c in metas}
all_c_id2c_borders.update(c_id2c_borders)
open_meta_ns(meta_graph, metas)
for c_id in c_id2info.keys():
(name, go, (l, out_c_id)) = c_id2info[c_id]
comp_n = comp_to_meta_node(meta_graph, c_id, go, name, out_c_id, False, n2xy)
if not comp_n:
continue
bend_edges(meta_graph)
color_edges(meta_graph)
export_edges(c_id2level2features, c_id2outs, meta_graph, processed, e2layout,
id2mask=id2mask)
metas = factor_nodes(meta_graph)
bend_ubiquitous_edges(meta_graph, metas)
bend_edges(meta_graph)
metas.append(comp_n)
color_edges(meta_graph)
export_edges(c_id2level2features, c_id2outs, meta_graph, processed, e2layout,
id2mask=id2mask)
open_meta_ns(meta_graph, metas)
return c_id2level2features, (n2layout, e2layout)
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)
def meta_graph2features(c_id2info,
c_id2outs,
meta_graph,
r2rs_ps,
n2xy=None,
id2mask=None,
onto=None):
root = meta_graph.getRoot()
c_id2level2features = {}
processed = set()
c_id2c_borders = {}
n2layout, e2layout = {}, {}
all_c_id2c_borders = {}
while True:
for c_id, sizes in c_id2c_borders.items():
layout_inner_elements(meta_graph, c_id, *sizes)
if n2xy:
apply_node_coordinates(meta_graph, n2xy)
bend_edges(meta_graph)
straighten_edges_inside_compartments(meta_graph, all_c_id2c_borders)
# bend_edges_around_compartments(meta_graph, (e for e in meta_graph.getEdges() if not get_e_id(e) in processed))
# bend_species_edges(meta_graph)
color_edges(meta_graph)
export_elements(c_id2info,
c_id2outs,
c_id2level2features,
meta_graph,
processed,
r2rs_ps,
n2layout,
e2layout,
id2mask=id2mask,
onto=onto)
metas = [
n for n in meta_graph.getNodes()
if meta_graph.isMetaNode(n) and TYPE_COMPARTMENT == root[TYPE][n]
]
if not metas:
c_id2c_borders = {}
metas = [
n for n in meta_graph.getNodes() if meta_graph.isMetaNode(n)
]
if not metas:
break
align_generalized_ns(meta_graph)
rotate_generalized_ns(meta_graph)
bend_ubiquitous_edges(meta_graph, metas)
else:
c_id2c_borders = {
root[ID][c]: get_comp_borders(c, root)
for c in metas
}
all_c_id2c_borders.update(c_id2c_borders)
open_meta_ns(meta_graph, metas)
for c_id in c_id2info.keys():
(name, go, (l, out_c_id)) = c_id2info[c_id]
comp_n = comp_to_meta_node(meta_graph, c_id, go, name, out_c_id, False,
n2xy)
if not comp_n:
continue
bend_edges(meta_graph)
color_edges(meta_graph)
export_edges(c_id2level2features,
c_id2outs,
meta_graph,
processed,
e2layout,
id2mask=id2mask)
metas = factor_nodes(meta_graph)
bend_ubiquitous_edges(meta_graph, metas)
bend_edges(meta_graph)
metas.append(comp_n)
color_edges(meta_graph)
export_edges(c_id2level2features,
c_id2outs,
meta_graph,
processed,
e2layout,
id2mask=id2mask)
open_meta_ns(meta_graph, metas)
return c_id2level2features, (n2layout, e2layout)