def graph2geojson(c_id2info, c_id2outs, graph, n2xy=None, colorer=color, id2mask=None, onto=None):
root = graph.getRoot()
logging.info('generalized species/reactions -> metanodes')
merge_ubs_for_similar_reactions(root)
r2rs_ps = get_reaction2reactants_products(root)
meta_graph = graph.inducedSubGraph([n for n in graph.getNodes()])
logging.info('compartments -> metanodes')
process_compartments(c_id2info, meta_graph, n2xy)
calculate_related_compartments(root)
colorer(root)
color_edges(root)
logging.info('tlp nodes -> geojson features')
c_id2level2features, (n2lo, e2lo) = meta_graph2features(c_id2info, c_id2outs, meta_graph, r2rs_ps, n2xy,
id2mask=id2mask, onto=onto)
geometry = geojson.Polygon([[0, DIMENSION], [0, 0], [DIMENSION, 0], [DIMENSION, DIMENSION]])
hidden_c_ids, c_id_hidden_ubs = filter_features(c_id2level2features)
rescale(c_id2level2features)
get_l2fs = lambda l2fs: {lev: geojson.FeatureCollection(features, geometry=geometry) for (lev, features) in
l2fs.items()}
return {c_id: get_l2fs(l2fs) for (c_id, l2fs) in c_id2level2features.items()}, (n2lo, e2lo), \
hidden_c_ids, c_id_hidden_ubs
def graph2geojson(c_id2info,
c_id2outs,
graph,
n2xy=None,
colorer=color,
id2mask=None,
onto=None):
root = graph.getRoot()
logging.info('generalized species/reactions -> metanodes')
merge_ubs_for_similar_reactions(root)
r2rs_ps = get_reaction2reactants_products(root)
meta_graph = graph.inducedSubGraph([n for n in graph.getNodes()])
logging.info('compartments -> metanodes')
process_compartments(c_id2info, meta_graph, n2xy)
calculate_related_compartments(root)
colorer(root)
color_edges(root)
logging.info('tlp nodes -> geojson features')
c_id2level2features, (n2lo, e2lo) = meta_graph2features(c_id2info,
c_id2outs,
meta_graph,
r2rs_ps,
n2xy,
id2mask=id2mask,
onto=onto)
geometry = geojson.Polygon([[0, DIMENSION], [0, 0], [DIMENSION, 0],
[DIMENSION, DIMENSION]])
hidden_c_ids, c_id_hidden_ubs = filter_features(c_id2level2features)
rescale(c_id2level2features)
get_l2fs = lambda l2fs: {
lev: geojson.FeatureCollection(features, geometry=geometry)
for (lev, features) in l2fs.items()
}
return {c_id: get_l2fs(l2fs) for (c_id, l2fs) in c_id2level2features.items()}, (n2lo, e2lo), \
hidden_c_ids, c_id_hidden_ubs
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 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)
